1
|
Dartsch RC, Kraut S, Mayer T, Gabel A, Dietrich A, Weissmann N, Fuchs B, Knoepp F. Use of FRET-Sensor 'Mermaid' to Detect Subtle Changes in Membrane Potential of Primary Mouse PASMCs. Cells 2024; 13:1070. [PMID: 38920698 PMCID: PMC11202191 DOI: 10.3390/cells13121070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Subtle changes in the membrane potential of pulmonary arterial smooth muscle cells (PASMCs) are pivotal for controlling pulmonary vascular tone, e.g., for initiating Hypoxic Pulmonary Vasoconstriction, a vital mechanism of the pulmonary circulation. In our study, we evaluated the ability of the fluorescence resonance energy transfer (FRET)-based voltage-sensor Mermaid to detect such subtle changes in membrane potential. Mouse PASMCs were isolated and transduced with Mermaid-encoding lentiviral vectors before the acceptor/donor emission ratio was assessed via live cell FRET-imaging. Mermaid's sensitivity was tested by applying specific potassium chloride (KCl) concentrations. These KCl concentrations were previously validated by patch clamp recordings to induce depolarization with predefined amplitudes that physiologically occur in PASMCs. Mermaid's emission ratio dose-dependently increased upon depolarization with KCl. However, Mermaid formed unspecific intracellular aggregates, which limited the usefulness of this voltage sensor. When analyzing the membrane rim only to circumvent these unspecific signals, Mermaid was not suitable to resolve subtle changes in the membrane potential of ≤10 mV. In summary, we found Mermaid to be a suitable alternative for reliably detecting qualitative membrane voltage changes of more than 10 mV in primary mouse PASMCs. However, one should be aware of the limitations associated with this voltage sensor.
Collapse
Affiliation(s)
- Ruth C. Dartsch
- Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, 35392 Giessen, Germany
| | - Simone Kraut
- Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, 35392 Giessen, Germany
| | - Tim Mayer
- Walther-Straub-Institute for Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians University, 80539 Munich, Germany; (T.M.)
| | - Andreas Gabel
- Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, 35392 Giessen, Germany
| | - Alexander Dietrich
- Walther-Straub-Institute for Pharmacology and Toxicology, Member of the German Center for Lung Research (DZL), Ludwig-Maximilians University, 80539 Munich, Germany; (T.M.)
| | - Norbert Weissmann
- Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, 35392 Giessen, Germany
| | - Beate Fuchs
- Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, 35392 Giessen, Germany
| | - Fenja Knoepp
- Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, 35392 Giessen, Germany
| |
Collapse
|
2
|
Gándara L, Durrieu L, Wappner P. Metabolic FRET sensors in intact organs: Applying spectral unmixing to acquire reliable signals. Biol Open 2023; 12:bio060030. [PMID: 37671927 PMCID: PMC10562930 DOI: 10.1242/bio.060030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
In multicellular organisms, metabolic coordination across multiple tissues and cell types is essential to satisfy regionalized energetic requirements and respond coherently to changing environmental conditions. However, most metabolic assays require the destruction of the biological sample, with a concomitant loss of spatial information. Fluorescent metabolic sensors and probes are among the most user-friendly techniques for collecting metabolic information with spatial resolution. In a previous work, we have adapted to an animal system, Drosophila melanogaster, genetically encoded metabolic FRET-based sensors that had been previously developed in single-cell systems. These sensors provide semi-quantitative data on the stationary concentrations of key metabolites of the bioenergetic metabolism: lactate, pyruvate, and 2-oxoglutarate. The use of these sensors in intact organs required the development of an image processing method that minimizes the contribution of spatially complex autofluorescence patterns, that would obscure the FRET signals. In this article, we show step by step how to design FRET-based sensor experiments and how to process the fluorescence signal to obtain reliable FRET values.
Collapse
Affiliation(s)
- Lautaro Gándara
- Fundación Instituto Leloir, Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Lucía Durrieu
- Fundación Instituto Leloir, Patricias Argentinas 435, Buenos Aires 1405, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales–Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425 Buenos Aires, Argentina
| | - Pablo Wappner
- Fundación Instituto Leloir, Patricias Argentinas 435, Buenos Aires 1405, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales–Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1425 Buenos Aires, Argentina
| |
Collapse
|
3
|
Shenberger Y, Gevorkyan-Airapetov L, Hirsch M, Hofmann L, Ruthstein S. An in-cell spin-labelling methodology provides structural information on cytoplasmic proteins in bacteria. Chem Commun (Camb) 2023; 59:10524-10527. [PMID: 37563959 DOI: 10.1039/d3cc03047d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
EPR in-cell spin-labeling was applied to CueR in E. coli. The methodology employed a Cu(II)-NTA complexed with dHis. High resolved in-cell distance distributions were obtained revealing minor differences between in vitro and in-cell data. This methodology allows study of structural changes of any protein in-cell, independent of size or cellular system.
Collapse
Affiliation(s)
- Yulia Shenberger
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Melanie Hirsch
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Lukas Hofmann
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences and Institute of Nanotechnology and Advanced Materials, Bar Ilan university, 5290002, Israel.
| |
Collapse
|
4
|
Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [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: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
Collapse
Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| |
Collapse
|
5
|
Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
Collapse
Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| |
Collapse
|
6
|
Abstract
Super-resolution fluorescence microscopy and Förster Resonance Energy Transfer (FRET) form a well-established family of techniques that has provided unique tools to study the dynamic architecture and functionality of biological systems, as well as to investigate nanomaterials. In the last years, the integration of super-resolution methods with FRET measurements has generated advances in two fronts. On the one hand, FRET-based probes have enhanced super-resolution imaging. On the other, the development of super-resolved FRET imaging methods has allowed the visualization of molecular interaction patterns with higher spatial resolution, less averaging and higher dynamic range. Here, we review these advances and discuss future perspectives, including the possible integration of FRET with next generation super-resolution techniques capable of reaching true molecular-scale spatial resolution.
Collapse
Affiliation(s)
- Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
| | - Cecilia Zaza
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
7
|
Liu Y, Zhang F, Jiang L, Perry JJP, Zhao Z, Liao J. Product inhibition kinetics determinations - Substrate interaction affinity and enzymatic kinetics using one quantitative FRET assay. Int J Biol Macromol 2021; 193:1481-1487. [PMID: 34780893 DOI: 10.1016/j.ijbiomac.2021.10.211] [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: 09/08/2021] [Accepted: 10/27/2021] [Indexed: 02/05/2023]
Abstract
Product inhibition is a common phenomenon during enzyme-catalyzed reactions. Almost all product molecules of an enzyme reaction should have some structural similarities to the substrate, and can thus still have affinities to the active site of the enzyme as product inhibitor. Currently, the characterizations of product inhibition are generally carried out by different methods to determine product binding affinity to the enzyme and the enzyme kinetics parameters, and then these parameters are combined to determine product inhibition. However, due to different sensitivity and variations, kinetics parameters determined from different methods are often not compatible, resulting in not accurate measurement. Here, we report a novel method that determines the two different classes of kinetics parameters, IC50 and Ki(or KD), Kcat and KM, using one single assay method-quantitative FRET(qFRET) assay for characterizing the product inhibition of pre-SUMO1's maturation by its protease SENP1. One method to determine all kinetics parameters provides, for the first time, not only a convenient method to determine all kinetics parameters, but more importantly, a novel approach to combine different measurements with mutually compatible results and errors.
Collapse
Affiliation(s)
- Yan Liu
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Fan Zhang
- State Key Laboratory of Oral Diseases, Department of Periodontology, National Clinical Research Center for Oral Diseases, West China, Hospital of Stomatology, Sichuan University, Chengdu, China; Physical Examination Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Jiang
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - J Jefferson P Perry
- City of Hope Biomedical Research Center, 1218 S. Fifth Avenue, Office 2268 Monrovia, CA 91016, USA
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases, Department of Periodontology, National Clinical Research Center for Oral Diseases, West China, Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA.
| |
Collapse
|
8
|
Liu Y, Shen Y, Song Y, Xu L, P. Perry JJ, Liao J. Isopeptidase Kinetics Determination by a Real Time and Sensitive qFRET Approach. Biomolecules 2021; 11:biom11050673. [PMID: 33946350 PMCID: PMC8145275 DOI: 10.3390/biom11050673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 02/05/2023] Open
Abstract
Isopeptidase activity of proteases plays critical roles in physiological and pathological processes in living organisms, such as protein stability in cancers and protein activity in infectious diseases. However, the kinetics of protease isopeptidase activity has not been explored before due to a lack of methodology. Here, we report the development of novel qFRET-based protease assay for characterizing the isopeptidase kinetics of SENP1. The reversible process of SUMOylation in vivo requires an enzymatic cascade that includes E1, E2, and E3 enzymes and Sentrin/SUMO-specific proteases (SENPs), which can act either as endopeptidases that process the pre-SUMO before its conjugation, or as isopeptidases to deconjugate SUMO from its target substrate. We first produced the isopeptidase substrate of CyPet-SUMO1/YPet-RanGAP1c by SUMOylation reaction in the presence of SUMO E1 and E2 enzymes. Then a qFRET analyses of real-time FRET signal reduction of the conjugated substrate of CyPet-SUMO1/YPet-RanGAP1c to free CyPet-SUMO1 and YPet-RanGAP1c by the SENP1 were able to obtain the kinetic parameters, Kcat, KM, and catalytic efficiency (Kcat/KM) of SENP1. This represents a pioneer effort in isopeptidase kinetics determination. Importantly, the general methodology of qFRET-based protease isopeptidase kinetic determination can also be applied to other proteases.
Collapse
Affiliation(s)
- Yan Liu
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (Y.L.); (Y.S.)
| | - Yali Shen
- Department of Abdominal Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Yang Song
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (Y.L.); (Y.S.)
| | - Lei Xu
- Department of Geography & the Environment, California State University, Fullerton, 800 N State College Blvd, Fullerton, CA 92831, USA;
| | - J. Jefferson P. Perry
- Department of Biochemistry, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: (J.J.P.P.); (J.L.)
| | - Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (Y.L.); (Y.S.)
- Department of Abdominal Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China;
- Department of Biochemistry, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: (J.J.P.P.); (J.L.)
| |
Collapse
|
9
|
Szalai AM, Siarry B, Lukin J, Giusti S, Unsain N, Cáceres A, Steiner F, Tinnefeld P, Refojo D, Jovin TM, Stefani FD. Super-resolution Imaging of Energy Transfer by Intensity-Based STED-FRET. NANO LETTERS 2021; 21:2296-2303. [PMID: 33621102 DOI: 10.1021/acs.nanolett.1c00158] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Förster resonance energy transfer (FRET) imaging methods provide unique insight into the spatial distribution of energy transfer and (bio)molecular interaction events, though they deliver average information for an ensemble of events included in a diffraction-limited volume. Coupling super-resolution fluorescence microscopy and FRET has been a challenging and elusive task. Here, we present STED-FRET, a method of general applicability to obtain super-resolved energy transfer images. In addition to higher spatial resolution, STED-FRET provides a more accurate quantification of interaction and has the capacity of suppressing contributions of noninteracting partners, which are otherwise masked by averaging in conventional imaging. The method capabilities were first demonstrated on DNA-origami model systems, verified on uniformly double-labeled microtubules, and then utilized to image biomolecular interactions in the membrane-associated periodic skeleton (MPS) of neurons.
Collapse
Affiliation(s)
- Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Bruno Siarry
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Jerónimo Lukin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Sebastián Giusti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Nicolás Unsain
- Laboratorio de Neurobiología, Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC, CONICET), Universidad Nacional de Córdoba (UNC), Friuli 2434, X5016NST Córdoba, Argentina
- Cátedra de Biología Celular y Molecular, Escuela de Biología, Centro de Biología Celular y Molecular (CeBiCeM, FCEFyN-UNC), Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, X5016NST Córdoba, Argentina
| | - Alfredo Cáceres
- Instituto Universitario de Ciencias Biomédicas Cordoba (IUCBC), Centro de Investigación Medicina Traslacional Severo Amuchástegui (CIMETSA), Friuli 2786, X5016NSW Córdoba, Argentina
| | - Florian Steiner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13 Haus E, 81377 München, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13 Haus E, 81377 München, Germany
| | - Damián Refojo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Thomas M Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Cátedra de Biología Celular y Molecular, Escuela de Biología; Centro de Biología Celular y Molecular (CeBiCeM, FCEFyN - UNC), Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Vélez Sarsfield 1611, X5016GCA, Córdoba, Argentina
| |
Collapse
|
10
|
Lone MS, Bhat PA, Afzal S, Chat OA, Dar AA. Energy transduction through FRET in self-assembled soft nanostructures based on surfactants/polymers: current scenario and prospects. SOFT MATTER 2021; 17:425-446. [PMID: 33400748 DOI: 10.1039/d0sm01625j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The self-assembled systems of surfactants/polymers, which are capable of supporting energy funneling between fluorophores, have recently gained significant attraction. Surfactant and polymeric micelles form nanoscale structures spanning a radius of 2-10 nm are generally suitable for the transduction of energy among fluorophores. These systems have shown great potential in Förster resonance energy transfer (FRET) due to their unique characteristics of being aqueous based, tendency to remain self-assembled, spontaneous formation, tunable nature, and responsiveness to different external stimuli. This review presents current developments in the field of energy transfer, particularly the multi-step FRET processes in the self-assembled nanostructures of surfactants/polymers. The part one of this review presents a background and brief overview of soft systems and discusses certain aspects of the self-assemblies of surfactants/polymers and their co-solubilization property to bring fluorophores to close proximity to transduce energy. The second part of this review deals with single-step and multi-step FRET in the self-assemblies of surfactants/polymers and links FRET systems with advanced smart technologies including multicolor formation, data encryption, and artificial antenna systems. This review also discusses the diverse examples in the literature to present the emerging applications of FRET. Finally, the prospects regarding further improvement of FRET in self-assembled soft systems are outlined.
Collapse
Affiliation(s)
- Mohd Sajid Lone
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
| | - Parvaiz Ahmad Bhat
- Department of Chemistry, Government Degree College, Pulwama-192301, J&K, India.
| | - Saima Afzal
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
| | - Oyais Ahmad Chat
- Department of Chemistry, Government Degree College, Pulwama-192301, J&K, India.
| | - Aijaz Ahmad Dar
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar-190006, J&K, India.
| |
Collapse
|
11
|
Fu Y, Liu X, Wang Y, He Y, Feng G, Wu H, Zheng C, Li P, Gan H. Miniaturized integrating sphere light sources based on LEDs for radiance responsivity calibration of optical imaging microscopes. OPTICS EXPRESS 2020; 28:32199-32213. [PMID: 33115182 DOI: 10.1364/oe.403899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
LED-based integrating sphere light sources (LED-ISLSs) in the size of typical microscope slides were developed to calibrate the radiance responsivity of optical imaging microscopes. Each LED-ISLS consists of a miniaturized integrating sphere with a diameter of 4 mm, an LED chip integrated on a printed circuit board, and a thin circular aperture with a diameter of 1 mm as the exit port. The non-uniformity of the radiant exitance of the LED-ISLSs was evaluated to be 0.8%. The normal radiance of the LED-ISLSs in the range of (5∼69) W m-2 sr-1 was measured with a standard uncertainty of 1.3% using two precision apertures and a standard silicon photodetector whose spectral responsivity is traceable to an absolute cryogenic radiometer. The LED-ISLSs were applied to calibrate the radiance responsivity of a home-built optical imaging microscope with a standard uncertainty of 2.6∼2.9%. The LED-ISLSs offer a practical way to calibrate the radiance responsivity of various optical imaging microscopes for results comparison and information exchange.
Collapse
|
12
|
The antifungal peptide CGA-N12 inhibits cell wall synthesis of Candida tropicalis by interacting with KRE9. Biochem J 2020; 477:747-762. [DOI: 10.1042/bcj20190678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/13/2019] [Accepted: 01/14/2020] [Indexed: 12/27/2022]
Abstract
CGA-N12, an antifungal peptide derived from chromogranin A, has specific antagonistic activity against Candida spp., especially against Candida tropicalis, by inducing cell apoptosis. However, the effect of CGA-N12 on the Candida cell wall is unknown. The Candida protein KRE9, which possesses β-1,6-glucanase activity, was screened by affinity chromatography after binding to CGA-N12. In this study, the effect of CGA-N12 on KRE9 and the interaction between CGA-N12 and KRE9 was studied to clarify the effect of CGA-N12 on C. tropicalis cell wall synthesis. The effect of CGA-N12 on recombinant KRE9 β-1,6-glucanase activity was investigated by analyzing the consumption of glucose. The results showed that CGA-N12 inhibited the activity of KRE9. After C. tropicalis was treated with CGA-N12, the structure of the C. tropicalis cell wall was damaged. The interaction between CGA-N12 and KRE9 was analyzed by isothermal titration calorimetry (ITC). The results showed that their interaction process was involved an endothermic reaction, and the interaction force was mainly hydrophobic with a few electrostatic forces. The results of the fluorescence resonance energy transfer (FRET) assay showed that the distance between CGA-N12 and KRE9 was 7 ∼ 10 nm during their interaction. Therefore, we concluded that the target of CGA-N12 in the C. tropicalis cell membrane is KRE9, and that CGA-N12 weakly binds to KRE9 within a 7 ∼ 10 nm distance and inhibits KRE9 activity.
Collapse
|
13
|
Lone MS, Afzal S, Chat OA, Bhat PA, Dutta R, Zhang Y, Kundu N, Dar AA. Broad Spectrum Tunable Photoluminescent Material Based on Cascade Fluorescence Resonance Energy Transfer between Three Fluorophores Encapsulated within the Self-Assembled Surfactant Systems. J Phys Chem B 2019; 123:9699-9711. [PMID: 31640345 DOI: 10.1021/acs.jpcb.9b07139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A broad spectrum tunable photoluminescent material with dual encryption based on a two-step fluorescence resonance energy transfer (FRET) between pyrene (Py), coumarin 480 (Cou480), and rhodamine 6G (R6G) in micelles of SDS and bmimDS is presented. The phenomenon is achievable due to the encapsulation of the fluorophores within these micelles. The transfer of energy as FRET between the pair Py and Cou480 showed ON at 336 nm and OFF at 402 nm in contrast to the FRET observed between the pair Cou480 and R6G that showed ON at 402 nm and OFF at 336 nm. However, the transfer of energy as FRET occurs from Py to R6G in the presence of Cou480 when excited at 336 nm, thereby making it a chain of three fluorophores with Cou480 acting as a relay fluorophore receiving energy from Py and transferring it to R6G. The different FRET scenarios between the three fluorophores in micelles provide a window for the generation of a matrix of colors, which occupies a significant 2D area in the chromaticity diagram, having potential applications in security printing. The different fluorophoric ratios generate different colors based on their individual photonic emissions and the FRET processes taking place between them. Writing tests were carried out using varied ratios of the fluorophores in the micellar systems producing different colored outputs under the UV light with insignificant visibility under the white light. We envision that this as-discovered three fluorophoric FRET system could form the basis for the future development of multi-FRET light-harvesting devices and anti-counterfeiting security inks based on much simpler non-covalent interaction aided encapsulation of the fluorophores within the self-assembled soft systems.
Collapse
Affiliation(s)
- Mohd Sajid Lone
- Physical Chemistry Division, Department of Chemistry , University of Kashmir , Hazratbal, Srinagar - 190006 , J&K , India
| | - Saima Afzal
- Physical Chemistry Division, Department of Chemistry , University of Kashmir , Hazratbal, Srinagar - 190006 , J&K , India
| | - Oyais Ahmad Chat
- Physical Chemistry Division, Department of Chemistry , University of Kashmir , Hazratbal, Srinagar - 190006 , J&K , India.,Department of Chemistry , Govt. Degree College Pulwama , Pulwama - 192301 , J&K , India
| | - Parvaiz Ahmad Bhat
- Department of Chemistry , Govt. Degree College Pulwama , Pulwama - 192301 , J&K , India
| | - Rupam Dutta
- Department of Chemistry , Indian Institute of Technology Kharagpur , Kharagpur - 721302 , West Bengal , India
| | - Yongliang Zhang
- Department of Chemical Engineering and Materials Science , University of Minnesota Twin Cities , 421 Washington Avenue , Minneapolis , Minnesota 55455 , United States
| | - Niloy Kundu
- Department of Chemistry , Indian Institute of Technology Kharagpur , Kharagpur - 721302 , West Bengal , India.,Environment Research Group, Research and Development , Tata Steel , Jamshedpur - 831001 , Jharkhand , India
| | - Aijaz Ahmad Dar
- Physical Chemistry Division, Department of Chemistry , University of Kashmir , Hazratbal, Srinagar - 190006 , J&K , India
| |
Collapse
|
14
|
Szendi-Szatmári T, Szabó Á, Szöllősi J, Nagy P. Reducing the Detrimental Effects of Saturation Phenomena in FRET Microscopy. Anal Chem 2019; 91:6378-6382. [DOI: 10.1021/acs.analchem.9b01504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tímea Szendi-Szatmári
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem Square 1, 4032 Debrecen, Hungary
| | - Ágnes Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem Square 1, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem Square 1, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem Square 1, 4032 Debrecen, Hungary
| |
Collapse
|
15
|
Weems JC, Unruh JR, Slaughter BD, Conaway RC, Conaway JW. Imaging-based assays for investigating functions of the RNA polymerase II elongation factor Elongin and the Elongin ubiquitin ligase. Methods 2019; 159-160:157-164. [DOI: 10.1016/j.ymeth.2019.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/03/2023] Open
|
16
|
Teunissen AJP, Pérez-Medina C, Meijerink A, Mulder WJM. Investigating supramolecular systems using Förster resonance energy transfer. Chem Soc Rev 2018; 47:7027-7044. [PMID: 30091770 PMCID: PMC6441672 DOI: 10.1039/c8cs00278a] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Supramolecular systems have applications in areas as diverse as materials science, biochemistry, analytical chemistry, and nanomedicine. However, analyzing such systems can be challenging due to the wide range of time scales, binding strengths, distances, and concentrations at which non-covalent phenomena take place. Due to their versatility and sensitivity, Förster resonance energy transfer (FRET)-based techniques are excellently suited to meet such challenges. Here, we detail the ways in which FRET has been used to study non-covalent interactions in both synthetic and biological supramolecular systems. Among other topics, we examine methods to measure molecular forces, determine protein conformations, monitor assembly kinetics, and visualize in vivo drug release from nanoparticles. Furthermore, we highlight multiplex FRET techniques, discuss the field's limitations, and provide a perspective on new developments.
Collapse
Affiliation(s)
- Abraham J. P. Teunissen
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Carlos Pérez-Medina
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Andries Meijerink
- Department of Chemistry, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Willem J. M. Mulder
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Laboratory of Chemical biology, Department of Biomedical Engineering and Institute for Complex Molecular systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, The Netherlands
| |
Collapse
|
17
|
Bezborodkina NN, Chestnova AY, Vorobev ML, Kudryavtsev BN. Spatial Structure of Glycogen Molecules in Cells. BIOCHEMISTRY (MOSCOW) 2018; 83:467-482. [PMID: 29738682 DOI: 10.1134/s0006297918050012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Glycogen is a strongly branched polymer of α-D-glucose, with glucose residues in the linear chains linked by 1→4-bonds (~93% of the total number of bonds) and with branching after every 4-8 residues formed by 1→6-glycosidic bonds (~7% of the total number of bonds). It is thought currently that a fully formed glycogen molecule (β-particle) with the self-glycosylating protein glycogenin in the center has a spherical shape with diameter of ~42 nm and contains ~ 55,000 glucose residues. The glycogen molecule also includes numerous proteins involved in its synthesis and degradation, as well as proteins performing a carcass function. However, the type and force of bonds connecting these proteins to the polysaccharide moiety of glycogen are significantly different. This review presents the available data on the spatial structure of the glycogen molecule and its changes under various physiological and pathological conditions.
Collapse
Affiliation(s)
- N N Bezborodkina
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia.
| | - A Yu Chestnova
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - M L Vorobev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| | - B N Kudryavtsev
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russia
| |
Collapse
|
18
|
Octeau JC, Chai H, Jiang R, Bonanno SL, Martin KC, Khakh BS. An Optical Neuron-Astrocyte Proximity Assay at Synaptic Distance Scales. Neuron 2018; 98:49-66.e9. [PMID: 29621490 PMCID: PMC5916847 DOI: 10.1016/j.neuron.2018.03.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/21/2018] [Accepted: 03/02/2018] [Indexed: 02/06/2023]
Abstract
Astrocytes are complex bushy cells that serve important functions through close contacts between their processes and synapses. However, the spatial interactions and dynamics of astrocyte processes relative to synapses have proven problematic to study in adult living brain tissue. Here, we report a genetically targeted neuron-astrocyte proximity assay (NAPA) to measure astrocyte-synapse spatial interactions within intact brain preparations and at synaptic distance scales. The method exploits resonance energy transfer between extracellularly displayed fluorescent proteins targeted to synapses and astrocyte processes. We validated the method in the striatal microcircuitry following in vivo expression. We determined the proximity of striatal astrocyte processes to distinct neuronal input pathways, to D1 and D2 medium spiny neuron synapses, and we evaluated how astrocyte-to-excitatory synapse proximity changed following cortical afferent stimulation, during ischemia and in a model of Huntington's disease. NAPA provides a simple approach to measure astrocyte-synapse spatial interactions in a variety of experimental scenarios. VIDEO ABSTRACT.
Collapse
Affiliation(s)
- J Christopher Octeau
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Hua Chai
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Ruotian Jiang
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Shivan L Bonanno
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Kelsey C Martin
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1751, USA
| | - Baljit S Khakh
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1751, USA; Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095-1751, USA.
| |
Collapse
|
19
|
Lisitsyna ES, Ketola TM, Morin-Picardat E, Liang H, Hanzlíková M, Urtti A, Yliperttula M, Vuorimaa-Laukkanen E. Time-Resolved Fluorescence Spectroscopy Reveals Fine Structure and Dynamics of Poly(l-lysine) and Polyethylenimine Based DNA Polyplexes. J Phys Chem B 2017; 121:10782-10792. [DOI: 10.1021/acs.jpcb.7b08394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ekaterina S. Lisitsyna
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| | - Tiia-Maaria Ketola
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| | - Emmanuelle Morin-Picardat
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Huamin Liang
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| | - Martina Hanzlíková
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Arto Urtti
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Marjo Yliperttula
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo, 5, 35131 Padova, Italy
| | - Elina Vuorimaa-Laukkanen
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| |
Collapse
|
20
|
Prost-Fingerle K, Hoffmann MD, Schützhold V, Cantore M, Fandrey J. Optical analysis of cellular oxygen sensing. Exp Cell Res 2017; 356:122-127. [DOI: 10.1016/j.yexcr.2017.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 03/07/2017] [Indexed: 12/22/2022]
|
21
|
Difference in the core-shell dynamics of polyethyleneimine and poly( l -lysine) DNA polyplexes. Eur J Pharm Sci 2017; 103:122-127. [DOI: 10.1016/j.ejps.2017.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/17/2017] [Accepted: 03/17/2017] [Indexed: 02/06/2023]
|
22
|
Obeng EM, Dullah EC, Razak NSA, Danquah MK, Budiman C, Ongkudon CM. Elucidating endotoxin-biomolecule interactions with FRET: extending the frontiers of their supramolecular complexation. J Biol Methods 2017; 4:e71. [PMID: 31453229 PMCID: PMC6706125 DOI: 10.14440/jbm.2017.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/24/2017] [Accepted: 02/28/2017] [Indexed: 01/22/2023] Open
Abstract
Endotoxin has been one of the topical chemical contaminants of major concern to researchers, especially in the field of bioprocessing. This major concern of researchers stems from the fact that the presence of Gram-negative bacterial endotoxin in intracellular products is unavoidable and requires complex downstream purification steps. For instance, endotoxin interacts with recombinant proteins, peptides, antibodies and aptamers and these interactions have formed the foundation for most biosensors for endotoxin detection. It has become imperative for researchers to engineer reliable means/techniques to detect, separate and remove endotoxin, without compromising the quality and quantity of the end-product. However, the underlying mechanism involved during endotoxin-biomolecule interaction is still a gray area. The use of quantitative molecular microscopy that provides high resolution of biomolecules is highly promising, hence, may lead to the development of improved endotoxin detection strategies in biomolecule preparation. Förster resonance energy transfer (FRET) spectroscopy is one of the emerging most powerful tools compatible with most super-resolution techniques for the analysis of molecular interactions. However, the scope of FRET has not been well-exploited in the analysis of endotoxin-biomolecule interaction. This article reviews endotoxin, its pathophysiological consequences and the interaction with biomolecules. Herein, we outline the common potential ways of using FRET to extend the current understanding of endotoxin-biomolecule interaction with the inference that a detailed understanding of the interaction is a prerequisite for the design of strategies for endotoxin identification and removal from protein milieus.
Collapse
Affiliation(s)
- Eugene M Obeng
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
| | - Elvina C Dullah
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
| | | | - Michael K Danquah
- Department of Chemical Engineering, Curtin University Sarawak, Miri, Sarawak 98009, Malaysia
| | - Cahyo Budiman
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
| |
Collapse
|
23
|
Hariri BM, McMahon DB, Chen B, Freund JR, Mansfield CJ, Doghramji LJ, Adappa ND, Palmer JN, Kennedy DW, Reed DR, Jiang P, Lee RJ. Flavones modulate respiratory epithelial innate immunity: Anti-inflammatory effects and activation of the T2R14 receptor. J Biol Chem 2017; 292:8484-8497. [PMID: 28373278 DOI: 10.1074/jbc.m116.771949] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/21/2017] [Indexed: 12/18/2022] Open
Abstract
Chronic rhinosinusitis has a significant impact on patient quality of life, creates billions of dollars of annual healthcare costs, and accounts for ∼20% of adult antibiotic prescriptions in the United States. Because of the rise of resistant microorganisms, there is a critical need to better understand how to stimulate and/or enhance innate immune responses as a therapeutic modality to treat respiratory infections. We recently identified bitter taste receptors (taste family type 2 receptors, or T2Rs) as important regulators of sinonasal immune responses and potentially important therapeutic targets. Here, we examined the immunomodulatory potential of flavones, a class of flavonoids previously demonstrated to have antibacterial and anti-inflammatory effects. Some flavones are also T2R agonists. We found that several flavones inhibit Muc5AC and inducible NOS up-regulation as well as cytokine release in primary and cultured airway cells in response to several inflammatory stimuli. This occurs at least partly through inhibition of protein kinase C and receptor tyrosine kinase activity. We also demonstrate that sinonasal ciliated epithelial cells express T2R14, which closely co-localizes (<7 nm) with the T2R38 isoform. Heterologously expressed T2R14 responds to multiple flavones. These flavones also activate T2R14-driven calcium signals in primary cells that activate nitric oxide production to increase ciliary beating and mucociliary clearance. TAS2R38 polymorphisms encode functional (PAV: proline, alanine, and valine at positions 49, 262, and 296, respectively) or non-functional (AVI: alanine, valine, isoleucine at positions 49, 262, and 296, respectively) T2R38. Our data demonstrate that T2R14 in sinonasal cilia is a potential therapeutic target for upper respiratory infections and that flavones may have clinical potential as topical therapeutics, particularly in T2R38 AVI/AVI individuals.
Collapse
Affiliation(s)
| | | | - Bei Chen
- Department of Otorhinolaryngology-Head and Neck Surgery
| | | | | | | | | | | | | | - Danielle R Reed
- Monell Chemical Senses Center, Philadelphia, Pennsylvania 19104
| | - Peihua Jiang
- Monell Chemical Senses Center, Philadelphia, Pennsylvania 19104
| | - Robert J Lee
- Department of Otorhinolaryngology-Head and Neck Surgery; Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia.
| |
Collapse
|
24
|
Graphene and graphene-like two-denominational materials based fluorescence resonance energy transfer (FRET) assays for biological applications. Biosens Bioelectron 2017; 89:123-135. [DOI: 10.1016/j.bios.2016.06.046] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 06/11/2016] [Accepted: 06/14/2016] [Indexed: 11/17/2022]
|
25
|
Liu Y, Shen Y, Zheng S, Liao J. A novel robust quantitative Förster resonance energy transfer assay for protease SENP2 kinetics determination against its all natural substrates. MOLECULAR BIOSYSTEMS 2016; 11:3407-14. [PMID: 26486594 DOI: 10.1039/c5mb00568j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
SUMOylation (the process of adding the SUMO [small ubiquitin-like modifier] to substrates) is an important post-translational modification of critical proteins in multiple processes. Sentrin/SUMO-specific proteases (SENPs) act as endopeptidases to process the pre-SUMO or as isopeptidases to deconjugate the SUMO from its substrate. Determining the kinetics of SENPs is important for understanding their activities. Förster resonance energy transfer (FRET) technology has been widely used in biomedical research and is a powerful tool for elucidating protein interactions. In this paper we report a novel quantitative FRET-based protease assay for SENP2 endopeptidase activity that accounts for the self-fluorescent emissions of the donor (CyPet) and the acceptor (YPet). The kinetic parameters, k(cat), K(M), and catalytic efficiency (k(cat)/K(M)) of catalytic domain SENP2 toward pre-SUMO1/2/3, were obtained by this novel design. Although we use SENP2 to demonstrate our method, the general principles of this quantitative FRET-based protease kinetic determination can be readily applied to other proteases.
Collapse
Affiliation(s)
- Yan Liu
- Department of Bioengineering, Bourns College of Engineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, USA.
| | - Yali Shen
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chngdu 610041, P. R. China
| | - Shasha Zheng
- Department of Health Sciences, College of Allied Health, California Baptist University, 8432 Magnolia Avenue, Riverside, CA 92504, USA
| | - Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, USA. and Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, California 92521, USA
| |
Collapse
|
26
|
Kraft LJ, Dowler J, Manral P, Kenworthy AK. Size, organization, and dynamics of soluble SQSTM1 and LC3-SQSTM1 complexes in living cells. Autophagy 2016; 12:1660-74. [PMID: 27442348 DOI: 10.1080/15548627.2016.1199299] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Selective macroautophagy/autophagy-with the help of molecular receptors-captures cargo for lysosomal degradation. Among the best-studied molecular receptors is SQSTM1/p62, a homo-oligomeric ubiquitin binding protein, which binds to both cargo and MAP1LC3B/LC3, a protein important for autophagosome biogenesis. Although the mechanisms underlying interaction of LC3 and SQSTM1 have been extensively studied, very little is known about the size or organization of soluble complexes formed between SQSTM1 and LC3 prior to phagophore (the autophagosome precursor) binding in live cells at the molecular level. To address this question, in the current study we use a combination of 2 microscopy-based approaches, FRET microscopy and confocal FRAP, to study the nanoscale properties of soluble SQSTM1 complexes and SQSTM1-LC3 complexes in living HeLa cells. We find that, independent of puncta, SQSTM1 oligomerizes to form very slowly diffusing complexes that contain multiple copies of SQSTM1 within FRET proximity of one another. Furthermore, we show that the interactions of soluble pools of LC3 and SQSTM1 can be readily detected by both FRAP and FRET. Finally, we uncover unexpected roles of SQSTM1's PB1 domain, a region of the protein involved in homo-oligomer formation, in complex formation. Taken together, these findings provide new insights into the nature of nanometer-sized protein complexes in the autophagy pathway.
Collapse
Affiliation(s)
- Lewis J Kraft
- a Chemical and Physical Biology Program , Vanderbilt University Medical Center , Nashville , TN , USA
| | - Jacob Dowler
- b Department of Molecular Physiology and Biophysics , Vanderbilt University Medical Center , Nashville , TN , USA
| | - Pallavi Manral
- b Department of Molecular Physiology and Biophysics , Vanderbilt University Medical Center , Nashville , TN , USA
| | - Anne K Kenworthy
- a Chemical and Physical Biology Program , Vanderbilt University Medical Center , Nashville , TN , USA.,b Department of Molecular Physiology and Biophysics , Vanderbilt University Medical Center , Nashville , TN , USA.,c Department of Cell and Developmental Biology , Vanderbilt University Medical Center , Nashville , TN , USA
| |
Collapse
|
27
|
Blaževitš O, Mideksa YG, Šolman M, Ligabue A, Ariotti N, Nakhaeizadeh H, Fansa EK, Papageorgiou AC, Wittinghofer A, Ahmadian MR, Abankwa D. Galectin-1 dimers can scaffold Raf-effectors to increase H-ras nanoclustering. Sci Rep 2016; 6:24165. [PMID: 27087647 PMCID: PMC4834570 DOI: 10.1038/srep24165] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 03/22/2016] [Indexed: 12/12/2022] Open
Abstract
Galectin-1 (Gal-1) dimers crosslink carbohydrates on cell surface receptors. Carbohydrate-derived inhibitors have been developed for cancer treatment. Intracellularly, Gal-1 was suggested to interact with the farnesylated C-terminus of Ras thus specifically stabilizing GTP-H-ras nanoscale signalling hubs in the membrane, termed nanoclusters. The latter activity may present an alternative mechanism for how overexpressed Gal-1 stimulates tumourigenesis. Here we revise the current model for the interaction of Gal-1 with H-ras. We show that it indirectly forms a complex with GTP-H-ras via a high-affinity interaction with the Ras binding domain (RBD) of Ras effectors. A computationally generated model of the Gal-1/C-Raf-RBD complex is validated by mutational analysis. Both cellular FRET as well as proximity ligation assay experiments confirm interaction of Gal-1 with Raf proteins in mammalian cells. Consistently, interference with H-rasG12V-effector interactions basically abolishes H-ras nanoclustering. In addition, an intact dimer interface of Gal-1 is required for it to positively regulate H-rasG12V nanoclustering, but negatively K-rasG12V nanoclustering. Our findings suggest stacked dimers of H-ras, Raf and Gal-1 as building blocks of GTP-H-ras-nanocluster at high Gal-1 levels. Based on our results the Gal-1/effector interface represents a potential drug target site in diseases with aberrant Ras signalling.
Collapse
Affiliation(s)
- Olga Blaževitš
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Yonatan G. Mideksa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Maja Šolman
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Alessio Ligabue
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Nicholas Ariotti
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Hossein Nakhaeizadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Eyad K. Fansa
- Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | | | | | - Mohammad R. Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| |
Collapse
|
28
|
A new trend to determine biochemical parameters by quantitative FRET assays. Acta Pharmacol Sin 2015; 36:1408-15. [PMID: 26567729 DOI: 10.1038/aps.2015.82] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 08/26/2015] [Indexed: 01/15/2023] Open
Abstract
Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research because it can determine molecule or particle interactions within a range of 1-10 nm. The sensitivity and efficiency of FRET strongly depend on the distance between the FRET donor and acceptor. Historically, FRET assays have been used to quantitatively deduce molecular distances. However, another major potential application of the FRET assay has not been fully exploited, that is, the use of FRET signals to quantitatively describe molecular interactive events. In this review, we discuss the use of quantitative FRET assays for the determination of biochemical parameters, such as the protein interaction dissociation constant (K(d)), enzymatic velocity (k(cat)) and K(m). We also describe fluorescent microscopy-based quantitative FRET assays for protein interaction affinity determination in cells as well as fluorimeter-based quantitative FRET assays for protein interaction and enzymatic parameter determination in solution.
Collapse
|
29
|
Rowland CE, Brown CW, Medintz IL, Delehanty JB. Intracellular FRET-based probes: a review. Methods Appl Fluoresc 2015; 3:042006. [PMID: 29148511 DOI: 10.1088/2050-6120/3/4/042006] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Probes that exploit Förster resonance energy transfer (FRET) in their feedback mechanism are touted for their sensitivity, robustness, and low background, and thanks to the exceptional distance dependence of the energy transfer process, they provide a means of probing lengthscales well below the resolution of light. These attributes make FRET-based probes superbly suited to an intracellular environment, and recent developments in biofunctionalization and expansion of imaging capabilities have put them at the forefront of intracellular studies. Here, we present an overview of the engineering and execution of a variety of recent intracellular FRET probes, highlighting the diversity of this class of materials and the breadth of application they have found in the intracellular environment.
Collapse
Affiliation(s)
- Clare E Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA. National Research Council, Washington, DC 20036, USA
| | | | | | | |
Collapse
|
30
|
Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015. [PMID: 26088273 DOI: 10.1103/revmodphys.87.1183] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
Collapse
Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
| |
Collapse
|
31
|
Moerner WEWE. Spektroskopie, Visualisierung und Photomanipulation einzelner Moleküle: die Grundlage für superhochauflösende Mikroskopie (Nobel-Aufsatz). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
32
|
Moerner WEWE. Single-Molecule Spectroscopy, Imaging, and Photocontrol: Foundations for Super-Resolution Microscopy (Nobel Lecture). Angew Chem Int Ed Engl 2015; 54:8067-93. [PMID: 26088273 DOI: 10.1002/anie.201501949] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/10/2022]
Abstract
The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90s, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later super-resolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized.
Collapse
Affiliation(s)
- W E William E Moerner
- Departments of Chemistry and (by Courtesy) of Applied Physics, Stanford University, Stanford, California 94305 (USA)
| |
Collapse
|
33
|
Finkbeiner S, Frumkin M, Kassner PD. Cell-based screening: extracting meaning from complex data. Neuron 2015; 86:160-74. [PMID: 25856492 PMCID: PMC4457442 DOI: 10.1016/j.neuron.2015.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 09/23/2014] [Accepted: 01/22/2015] [Indexed: 01/23/2023]
Abstract
Unbiased discovery approaches have the potential to uncover neurobiological insights into CNS disease and lead to the development of therapies. Here, we review lessons learned from imaging-based screening approaches and recent advances in these areas, including powerful new computational tools to synthesize complex data into more useful knowledge that can reliably guide future research and development.
Collapse
Affiliation(s)
- Steven Finkbeiner
- Director of the Taube/Koret Center for Neurodegenerative Disease and the Hellman Family Foundation Program in Alzheimer's Disease Research, Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Michael Frumkin
- Director of Engineering, Research, Google, Inc., 1600 Amphitheatre Parkway, Mountain View, CA 94043, USA
| | - Paul D Kassner
- Director of Research, Amgen, Inc., 1120 Veterans Boulevard South, San Francisco, CA 94080, USA
| |
Collapse
|
34
|
Duwé S, Moeyaert B, Dedecker P. Diffraction-unlimited fluorescence microscopy of living biological samples using pcSOFI. ACTA ACUST UNITED AC 2015; 7:27-41. [PMID: 25727061 DOI: 10.1002/9780470559277.ch140025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The complex microscopic nature of many live biological processes is often obscured by the diffraction limit of light, requiring diffraction-unlimited fluorescence microscopy to resolve them. Because of the vast range of different processes that can be studied, sub-diffraction imaging should work efficiently under many different conditions. Photochromic stochastic optical fluctuation imaging (pcSOFI) is a recent addition to the field of diffraction-unlimited fluorescence microscopy. This robust and versatile method employs a statistical analysis of random fluctuations in the emission of single labels, in this case reversibly switchable fluorescent proteins (RSFPs), to retrieve super-resolution information. Added to the resolution enhancement, pcSOFI also offers contrast enhancement and background reduction in a practical and convenient way. Here, we describe the necessary steps to obtain diffraction-unlimited images, including multicolor and three-dimensional imaging, and highlight the advantages of pcSOFI together with the circumstances under which pcSOFI can be favorably applied.
Collapse
Affiliation(s)
- Sam Duwé
- Department of Chemistry, University of Leuven, Heverlee, Belgium
| | | | | |
Collapse
|
35
|
Lu M, Lu HP. Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy. J Phys Chem B 2014; 118:11943-55. [PMID: 25222115 PMCID: PMC4199541 DOI: 10.1021/jp5081498] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Conformational motions of proteins
are highly dynamic and intrinsically
complex. To capture the temporal and spatial complexity of conformational
motions and further to understand their roles in protein functions,
an attempt is made to probe multidimensional conformational dynamics
of proteins besides the typical one-dimensional FRET coordinate or
the projected conformational motions on the one-dimensional FRET coordinate.
T4 lysozyme hinge-bending motions between two domains along α-helix
have been probed by single-molecule FRET. Nevertheless, the domain
motions of T4 lysozyme are rather complex involving multiple coupled
nuclear coordinates and most likely contain motions besides hinge-bending.
It is highly likely that the multiple dimensional protein conformational
motions beyond the typical enzymatic hinged-bending motions have profound
impact on overall enzymatic functions. In this report, we have developed
a single-molecule multiparameter photon stamping spectroscopy integrating
fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic
approach enables simultaneous observations of both FRET-related site-to-site
conformational dynamics and molecular rotational (or orientational)
motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have
further observed wide-distributed rotational flexibility along orientation
coordinates by recording fluorescence anisotropy and simultaneously
identified multiple intermediate conformational states along FRET
coordinate by monitoring time-dependent donor lifetime, presenting
a whole picture of multidimensional conformational dynamics in the
process of T4 lysozyme open-close hinge-bending enzymatic turnover
motions under enzymatic reaction conditions. By analyzing the autocorrelation
functions of both lifetime and anisotropy trajectories, we have also
observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional
conformational fluctuation dynamics, providing a fundamental understanding
of the enzymatic reaction turnover dynamics associated with overall
enzyme as well as the specific active-site conformational fluctuations
that are not identifiable and resolvable in the conventional ensemble-averaged
experiment.
Collapse
Affiliation(s)
- Maolin Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | | |
Collapse
|
36
|
Coltharp C, Yang X, Xiao J. Quantitative analysis of single-molecule superresolution images. Curr Opin Struct Biol 2014; 28:112-21. [PMID: 25179006 DOI: 10.1016/j.sbi.2014.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
Abstract
This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10-50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images.
Collapse
Affiliation(s)
- Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
37
|
Malik-Chaudhry HK, Saavedra A, Liao J. A linker strategy for trans-FRET assay to determine activation intermediate of NEDDylation cascade. Biotechnol Bioeng 2014; 111:1288-95. [PMID: 24415255 DOI: 10.1002/bit.25183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/27/2013] [Accepted: 01/03/2014] [Indexed: 11/10/2022]
Abstract
Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research and is a valuable tool for elucidating molecular interactions in vitro and in vivo. Quantitative FRET analysis is a powerful method for determining biochemical parameters and molecular distances at nanometer levels. Recently, we reported theoretical developments and experimental procedures for determining the dissociation constant, Kd and enzymatic kinetics parameters, Kcat and KM, of protein interactions with the engineered FRET pair, CyPet and YPet. The strong FRET signal from this pair made these developments possible. However, the direct link of fluorescent proteins with proteins of interests may interfere with the folding of some fusion proteins. Here, we report a new protein engineering strategy for improving FRET signals by adding a linker between the fluorescent protein and the targeted protein. This improvement allowed us to follow the covalent conjugation of NEDD8 to its E2 ligase in the presence of E1 and ATP, which was difficult to determine without linker. Three linkers, LAEAAAKEAA, TSGSPGLQEFGT, and LAAALAAA, which are alpha helix or random coil, all significantly improved the FRET signals. Our results show a general methodology for improving trans-FRET signals to effectively determine biochemical reaction intermediates.
Collapse
Affiliation(s)
- Harbani Kaur Malik-Chaudhry
- Department of Bioengineering, Center for Bioengineering Research, Bourns College of Engineering, 900 University Avenue, Riverside, California, 92521
| | | | | |
Collapse
|
38
|
RUEDAS-RAMA MJ, ALVAREZ-PEZ JM, ORTE A. SOLVING SINGLE BIOMOLECULES BY ADVANCED FRET-BASED SINGLE-MOLECULE FLUORESCENCE TECHNIQUES. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013300041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The use of Förster resonance energy transfer (FRET) has undergone a renaissance in the last two decades, especially in the study of structure of biomolecules, biomolecular interactions, and dynamics. Thanks to powerful advances in single-molecule fluorescence (SMF) techniques, seeing molecules at work is a reality, which has helped to build up the mindset of molecular machines. In the last few years, many technical developments have broadened the applications of SMF-FRET, expanding the amount of information that can be recovered from individual molecules. Here, we focus on the non-standard SMF-FRET techniques, such as two-color coincidence detection (TCCD), alternating laser excitation (ALEX), multiparameter fluorescence detection (MFD); the addition of fluorescence lifetime as an orthogonal dimension in single-molecule experiments; or the development of novel and improved methods of analysis constituting to a set of advanced methodologies that may become routine tools in a close future. [Formula: see text]Special Issue Comment: This review about advanced single-molecule FRET techniques is specially related to the review by Jørgensen and Hatzakis,6 who detail experimetal strategies to solve the activity of single enzymes. The advanced techniques described in our paper may serve as interesting alternatives when applied to enzyme studies. Our manuscript is also related to the reviews in this Special Issue that deal with model solving.22,130
Collapse
Affiliation(s)
- M. J. RUEDAS-RAMA
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Cartuja Campus, Granada, 18071, Spain
| | - J. M. ALVAREZ-PEZ
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Cartuja Campus, Granada, 18071, Spain
| | - A. ORTE
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Cartuja Campus, Granada, 18071, Spain
| |
Collapse
|
39
|
Alouini MA, Moustoifa EF, Rubio-Albenque S, Berthelot T, Fery-Forgues S, Déléris G. Interaction of Fluorescently Labeled Triethyleneglycol and Peptide Derivatives with β-Cyclodextrin. Chemphyschem 2014; 15:444-57. [DOI: 10.1002/cphc.201301032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Indexed: 11/08/2022]
|
40
|
Abstract
Optical microscopy has developed as an indispensable tool for Arabidopsis cell biology. This is due to the high sensitivity, good spatial resolution, minimal invasiveness, and availability of autofluorescent proteins, which can be specifically fused to a distinct protein of interest. In this chapter, we introduce the theoretical concepts of fluorescence emission necessary to accomplish quantitative and functional cell biology using optical microscopy. The main focus lies on spectroscopic techniques, which, in addition to intensity-based studies, provide functional insight into cellular processes.
Collapse
|
41
|
Ellinger D, Voigt CA. The use of nanoscale fluorescence microscopic to decipher cell wall modifications during fungal penetration. FRONTIERS IN PLANT SCIENCE 2014; 5:270. [PMID: 24995012 PMCID: PMC4061529 DOI: 10.3389/fpls.2014.00270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 05/25/2014] [Indexed: 05/08/2023]
Abstract
Plant diseases are one of the most studied subjects in the field of plant science due to their impact on crop yield and food security. Our increased understanding of plant-pathogen interactions was mainly driven by the development of new techniques that facilitated analyses on a subcellular and molecular level. The development of labeling technologies, which allowed the visualization and localization of cellular structures and proteins in live cell imaging, promoted the use of fluorescence and laser-scanning microscopy in the field of plant-pathogen interactions. Recent advances in new microscopic technologies opened their application in plant science and in the investigation of plant diseases. In this regard, in planta Förster/Fluorescence resonance energy transfer has demonstrated to facilitate the measurement of protein-protein interactions within the living tissue, supporting the analysis of regulatory pathways involved in plant immunity and putative host-pathogen interactions on a nanoscale level. Localization microscopy, an emerging, non-invasive microscopic technology, will allow investigations with a nanoscale resolution leading to new possibilities in the understanding of molecular processes.
Collapse
Affiliation(s)
| | - Christian A. Voigt
- *Correspondence: Christian A. Voigt, Phytopathology and Biochemistry, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststrasse 18, 22609 Hamburg, Germany e-mail:
| |
Collapse
|
42
|
Jiang L, Saavedra AN, Way G, Alanis J, Kung R, Li J, Xiang W, Liao J. Specific substrate recognition and thioester intermediate determinations in ubiquitin and SUMO conjugation cascades revealed by a high-sensitive FRET assay. MOLECULAR BIOSYSTEMS 2014; 10:778-86. [DOI: 10.1039/c3mb70155g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
43
|
A novel homogeneous immunoassay for anthrax detection based on the AlphaLISA method: detection of B. anthracis spores and protective antigen (PA) in complex samples. Anal Bioanal Chem 2013; 405:3965-72. [DOI: 10.1007/s00216-013-6752-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 12/17/2012] [Accepted: 01/16/2013] [Indexed: 02/07/2023]
|
44
|
Cho S, Jang J, Song C, Lee H, Ganesan P, Yoon TY, Kim MW, Choi MC, Ihee H, Heo WD, Park Y. Simple super-resolution live-cell imaging based on diffusion-assisted Förster resonance energy transfer. Sci Rep 2013; 3:1208. [PMID: 23383376 PMCID: PMC3563037 DOI: 10.1038/srep01208] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/04/2013] [Indexed: 12/31/2022] Open
Abstract
Despite the recent development of several super-resolution fluorescence microscopic techniques, there are still few techniques that can be readily employed in conventional imaging systems. We present a very simple, rapid, general and cost-efficient super-resolution imaging method, which can be directly employed in a simple fluorescent imaging system with general fluorophores. Based on diffusion-assisted Förster resonance energy transfer (FRET), fluorescent donor molecules that label specific target structures can be stochastically quenched by diffusing acceptor molecules, thereby temporally separating otherwise spatially overlapped fluorescence signals and allowing super-resolution imaging. The proposed method provides two- to three-fold-enhancement in spatial resolution, a significant optical sectioning property, and favorable temporal resolution in live-cell imaging. We demonstrate super-resolution live-cell dynamic imaging using general fluorophores in a standard epi-fluorescence microscope with light-emitting diode (LED) illumination. Due to the simplicity of this approach, we expect that the proposed method will prove an attractive option for super-resolution imaging.
Collapse
Affiliation(s)
- Sangyeon Cho
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Mondal S, Das T, Ghosh P, Maity A, Mallick A, Purkayastha P. FRET-based characterisation of surfactant bilayer protected core–shell carbon nanoparticles: advancement toward carbon nanotechnology. Chem Commun (Camb) 2013; 49:7638-40. [DOI: 10.1039/c3cc43443e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
46
|
Geißler D, Stufler S, Löhmannsröben HG, Hildebrandt N. Six-Color Time-Resolved Förster Resonance Energy Transfer for Ultrasensitive Multiplexed Biosensing. J Am Chem Soc 2012; 135:1102-9. [DOI: 10.1021/ja310317n] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel Geißler
- Physical Chemistry, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Stefan Stufler
- NanoPolyPhotonics, Fraunhofer Institute for Applied Polymer Research,
14476 Potsdam-Golm, Germany
| | | | - Niko Hildebrandt
- Institut d’Electronique
Fondamentale, Université Paris-Sud, 91405 Orsay Cedex, France
| |
Collapse
|
47
|
Šimková E, Staněk D. Probing nucleic acid interactions and pre-mRNA splicing by Förster Resonance Energy Transfer (FRET) microscopy. Int J Mol Sci 2012; 13:14929-45. [PMID: 23203103 PMCID: PMC3509619 DOI: 10.3390/ijms131114929] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 01/11/2023] Open
Abstract
Förster resonance energy transfer (FRET) microscopy is a powerful technique routinely used to monitor interactions between biomolecules. Here, we focus on the techniques that are used for investigating the structure and interactions of nucleic acids (NAs). We present a brief overview of the most commonly used FRET microscopy techniques, their advantages and drawbacks. We list experimental approaches recently used for either in vitro or in vivo studies. Next, we summarize how FRET contributed to the understanding of pre-mRNA splicing and spliceosome assembly.
Collapse
Affiliation(s)
- Eva Šimková
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic; E-Mail:
| | - David Staněk
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic; E-Mail:
| |
Collapse
|
48
|
Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012; 13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
Collapse
Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | | |
Collapse
|
49
|
Gandhi M, Evdokimova V, Nikiforov YE. Frequency of close positioning of chromosomal loci detected by FRET correlates with their participation in carcinogenic rearrangements in human cells. Genes Chromosomes Cancer 2012; 51:1037-44. [PMID: 22887574 DOI: 10.1002/gcc.21988] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 07/01/2012] [Indexed: 11/05/2022] Open
Abstract
It has been well established that genes participating in oncogenic rearrangements are non-randomly positioned and frequently close to each other in human cell nuclei. However, the actual distance between these fusion partners has never been determined. The phenomenon of fluorescence resonance energy transfer (FRET) is observed when a donor fluorophore is close (<10 nm) to transfer some of it energy to an acceptor fluorophore. The aim of this study was to validate the use of FRET on directly labeled DNA molecules to assess the frequency of positioning at <10 nm distances between genes known to be involved in rearrangement and to correlate it with their probability to undergo rearrangement. In the validation experiments, the frequency of FRET-sensitized emission (SE) was found to be 93-96% between probes for the immediately adjacent chromosomal regions as compared to 0.1-0.2% between probes for the random loci located on large linear separation. Further, we found that the frequency of FRET-SE between four pairs of genes that form rearrangements in thyroid cancer was 5% for RET and CCDC6, 4% for RET and NCOA4, 2% for BRAF and AKAP9, and 2% for NTRK1 and TPR. Moreover, the frequency with which FRET was observed showed strong correlation (r = 0.9871) with the prevalence of respective rearrangements in thyroid cancer. Our findings demonstrate that FRET can be used as a technique to analyze proximity between specific DNA regions and that the frequency of gene positioning at distances allowing FRET correlates with their probability to undergo chromosomal rearrangements.
Collapse
Affiliation(s)
- Manoj Gandhi
- Department of Pathology, University of Pittsburgh, PA 15261, USA
| | | | | |
Collapse
|
50
|
LI-cadherin cis-dimerizes in the plasma membrane Ca(2+) independently and forms highly dynamic trans-contacts. Cell Mol Life Sci 2012; 69:3851-62. [PMID: 22842778 PMCID: PMC3478510 DOI: 10.1007/s00018-012-1053-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/22/2012] [Accepted: 06/06/2012] [Indexed: 11/25/2022]
Abstract
LI-cadherin belongs to the family of 7D-cadherins that is characterized by a low sequence similarity to classical cadherins, seven extracellular cadherin repeats (ECs), and a short cytoplasmic domain. Nevertheless, LI-cadherins mediates Ca2+-dependent cell–cell adhesion and induces an epitheloid cellular phenotype in non-polarized CHO cells. Whereas several studies suggest that classical cadherins cis-dimerize in a Ca2+-dependent manner and interact in trans by strand-swapping tryptophan 2 of EC1, little is known about the molecular interactions of LI-cadherin, which lacks tryptophan 2. We thus expressed fluorescent LI-cadherin fusion proteins in HEK293 and CHO cells, analyzed their cell–cell adhesive properties and studied their cellular distribution, cis-interaction, and lateral diffusion in the presence and absence of Ca2+. LI-cadherin highly concentrates in cell contact areas but rapidly leaves those sites upon Ca2+ depletion and redistributes evenly on the cell surface, indicating that it is only kept in the contact areas by trans-interactions. Fluorescence resonance energy transfer analysis of LI-cadherin-CFP and -YFP revealed that LI-cadherin forms cis-dimers that resist Ca2+ depletion. As determined by fluorescence redistribution after photobleaching, LI-cadherin freely diffuses in the plasma membrane as a cis-dimer (D = 0.42 ± 0.03 μm2/s). When trapped by trans-binding in cell contact areas, its diffusion coefficient decreases only threefold to D = 0.12 ± 0.01 μm2/s, revealing that, in contrast to classical and desmosomal cadherins, trans-contacts formed by LI-cadherin are highly dynamic.
Collapse
|