1
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Nordahl L, Akkuratov EE, Heimgärtner J, Schach K, Meineke B, Elsässer S, Wennmalm S, Brismar H. Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS. Biochim Biophys Acta Gen Subj 2024; 1868:130619. [PMID: 38643888 DOI: 10.1016/j.bbagen.2024.130619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
The sodium potassium pump, Na,K-ATPase (NKA), is an integral plasma membrane protein, expressed in all eukaryotic cells. It is responsible for maintaining the transmembrane Na+ gradient and is the major determinant of the membrane potential. Self-interaction and oligomerization of NKA in cell membranes has been proposed and discussed but is still an open question. Here, we have used a combination of FRET and Fluorescence Correlation Spectroscopy, FRET-FCS, to analyze NKA in the plasma membrane of living cells. Click chemistry was used to conjugate the fluorescent labels Alexa 488 and Alexa 647 to non-canonical amino acids introduced in the NKA α1 and β1 subunits. We demonstrate that FRET-FCS can detect an order of magnitude lower concentration of green-red labeled protein pairs in a single-labeled red and green background than what is possible with cross-correlation (FCCS). We show that a significant fraction of NKA is expressed as a dimer in the plasma membrane. We also introduce a method to estimate not only the number of single and double labeled NKA, but the number of unlabeled, endogenous NKA and estimate the density of endogenous NKA at the plasma membrane to 1400 ± 800 enzymes/μm2.
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Affiliation(s)
- Linnea Nordahl
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
| | - Evgeny E Akkuratov
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Johannes Heimgärtner
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Katja Schach
- Graduate Training Centre of Neuroscience, University of Tübingen, Otfried-Müller-Str. 27, 72076 Tübingen, Germany
| | - Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Simon Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Stefan Wennmalm
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
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2
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Flores-Hernandez DR, Santamaria-Garcia VJ, Melchor-Martínez EM, Sosa-Hernández JE, Parra-Saldívar R, Bonilla-Rios J. Paper and Other Fibrous Materials-A Complete Platform for Biosensing Applications. BIOSENSORS 2021; 11:128. [PMID: 33919464 PMCID: PMC8143474 DOI: 10.3390/bios11050128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/22/2023]
Abstract
Paper-based analytical devices (PADs) and Electrospun Fiber-Based Biosensors (EFBs) have aroused the interest of the academy and industry due to their affordability, sensitivity, ease of use, robustness, being equipment-free, and deliverability to end-users. These features make them suitable to face the need for point-of-care (POC) diagnostics, monitoring, environmental, and quality food control applications. Our work introduces new and experienced researchers in the field to a practical guide for fibrous-based biosensors fabrication with insight into the chemical and physical interaction of fibrous materials with a wide variety of materials for functionalization and biofunctionalization purposes. This research also allows readers to compare classical and novel materials, fabrication techniques, immobilization methods, signal transduction, and readout. Moreover, the examined classical and alternative mathematical models provide a powerful tool for bioanalytical device designing for the multiple steps required in biosensing platforms. Finally, we aimed this research to comprise the current state of PADs and EFBs research and their future direction to offer the reader a full insight on this topic.
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Affiliation(s)
| | | | | | | | | | - Jaime Bonilla-Rios
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Avenida Eugenio Garza Sada 2501, Monterrey 64849, NL, Mexico; (D.R.F.-H.); (V.J.S.-G.); (E.M.M.-M.); (J.E.S.-H.); (R.P.-S.)
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3
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Sreenivasan VKA, Graus MS, Pillai RR, Yang Z, Goyette J, Gaus K. Influence of FRET and fluorescent protein maturation on the quantification of binding affinity with dual-channel fluorescence cross-correlation spectroscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:6137-6153. [PMID: 33282480 PMCID: PMC7687962 DOI: 10.1364/boe.401056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 06/12/2023]
Abstract
Protein-protein interactions at the plasma membrane mediate transmembrane signaling. Dual-channel fluorescence cross-correlation spectroscopy (dc-FCCS) is a method with which these interactions can be quantified in a cellular context. However, factors such as incomplete maturation of fluorescent proteins, spectral crosstalk, and fluorescence resonance energy transfer (FRET) affect quantification. Some of these can be corrected or accounted for during data analysis and/or interpretation. Here, we experimentally and analytically demonstrate that it is difficult to correct the error caused due to FRET when applying dc-FCCS to measure binding affinity or bound molecular concentrations. Additionally, the presence of dark fluorescent proteins due to incomplete maturation introduces further errors, which too cannot be corrected in the presence of FRET. Based on simulations, we find that modalities such as pulse-interleaved excitation FCCS do not eliminate FRET-induced errors. Finally, we demonstrate that the detrimental effect of FRET can be eliminated with careful experimental design when applying dc-FCCS to quantify protein-protein interactions at the plasma membrane of living cells.
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Affiliation(s)
- Varun K A Sreenivasan
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Matthew S Graus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Rashmi R Pillai
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Zhengmin Yang
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
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4
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Wang Y, Zhang Z, Zhang Y, Yu C. A real-time fluorescence assay for protease activity and inhibitor screening based on the aggregation-caused quenching of a perylene probe. LUMINESCENCE 2018; 33:790-796. [PMID: 29607616 DOI: 10.1002/bio.3478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 02/04/2018] [Accepted: 02/10/2018] [Indexed: 01/01/2023]
Abstract
We have established a real-time and label-free fluorescence turn-on strategy for protease activity detection and inhibitor screening via peptide-induced aggregation-caused quenching of a perylene probe. Because of electrostatic interactions and high hydrophilicity, poly-l-glutamic acid sodium salt (PGA; a negatively charged peptide) could induce aggregation of a positively charged perylene probe (probe 1) and the monomer fluorescence of probe 1 was effectively quenched. After a protease was added, PGA was enzymatically hydrolyzed into small fragments and probe 1 disaggregated. The fluorescence recovery of probe 1 was found to be proportional to the concentration of protease in the range from 0 to 1 mU/ml. The detection limit was down to 0.1 mU/ml. In the presence of a protease inhibitor, protease activity was inhibited and fluorescence recovery reduced. Moreover, we demonstrated the potential application of our method in a complex mixture sample including 1% human serum. Our method is simple, fast and cost effective.
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Affiliation(s)
- Yan Wang
- School of Chemistry and Chemical Engineering, Yulin University, Shaanxi, Yulin, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, People's Republic of China
| | - Zhifang Zhang
- School of Chemistry and Chemical Engineering, Yulin University, Shaanxi, Yulin, People's Republic of China
| | - Ya Zhang
- School of Chemistry and Chemical Engineering, Yulin University, Shaanxi, Yulin, People's Republic of China
| | - Cong Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, People's Republic of China
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5
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Deciphering CaMKII Multimerization Using Fluorescence Correlation Spectroscopy and Homo-FRET Analysis. Biophys J 2017; 112:1270-1281. [PMID: 28355553 DOI: 10.1016/j.bpj.2017.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/03/2017] [Accepted: 02/03/2017] [Indexed: 11/20/2022] Open
Abstract
While kinases are typically composed of one or two subunits, calcium-calmodulin (CaM)-dependent protein kinase II (CaMKII) is composed of 8-14 subunits arranged as pairs around a central core. It is not clear if the CaMKII holoenzyme functions as an assembly of independent subunits, as catalytic pairs, or as a single unit. One strategy to address this question is to genetically engineer monomeric and dimeric CaMKII and evaluate how their activity compares to the wild-type (WT) holoenzyme. Here a technique that combines fluorescence correlation spectroscopy and homo-FRET analysis was used to characterize assembly mutants of Venus-tagged CaMKIIα to identify a dimeric CaMKII. Spectroscopy was then used to compare how holoenzyme structure and function changes in response to activation with CaM in the dimeric mutant, WT-holoenzyme, and a monomeric CaMKII oligomerization-domain deletion mutant control. CaM triggered an increase in hydrodynamic volume in both WT and dimeric CaMKII without altering subunit stoichiometry or the net homo-FRET between Venus-tagged catalytic domains. Biochemical analysis revealed that the dimeric mutant also functioned like WT holoenzyme in terms of its kinase activity with an exogenous substrate, and for endogenous T286 autophosphorylation. We conclude that the fundamental functional units of CaMKII holoenzyme are paired catalytic-domains.
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6
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Wennmalm S, Chmyrov V, Widengren J, Tjernberg L. Highly Sensitive FRET-FCS Detects Amyloid β-Peptide Oligomers in Solution at Physiological Concentrations. Anal Chem 2015; 87:11700-5. [PMID: 26489794 DOI: 10.1021/acs.analchem.5b02630] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligomers formed by the amyloid β-peptide (Aβ) are pathogens in Alzheimer's disease. Increased knowledge on the oligomerization process is crucial for understanding the disease and for finding treatments. Ideally, Aβ oligomerization should be studied in solution and at physiologically relevant concentrations, but most popular techniques of today are not capable of such analyses. We demonstrate here that the combination of Förster Resonance Energy Transfer and Fluorescence Correlation Spectroscopy (FRET-FCS) has a unique ability to detect small subpopulations of FRET-active molecules and oligomers. FRET-FCS could readily detect a FRET-active oligonucleotide present at levels as low as 0.5% compared to FRET-inactive dye molecules. In contrast, three established fluorescence fluctuation techniques (FCS, FCCS, and PCH) required fractions between 7 and 11%. When applied to the analysis of Aβ, FRET-FCS detected oligomers consisting of less than 10 Aβ molecules, which coexisted with the monomers at fractions as low as 2 ± 2%. Thus, we demonstrate for the first time direct detection of small fractions of Aβ oligomers in solution at physiological concentrations. This ability of FRET-FCS could be an indispensable tool for studying biological oligomerization processes, in general, and for finding therapeutically useful oligomerization inhibitors.
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Affiliation(s)
- Stefan Wennmalm
- Royal Institute of Technology-KTH, Department of Applied Physics, Experimental Biomolecular Physics Group, Scilifelab , 171 65 Solna, Sweden
| | - Volodymyr Chmyrov
- Royal Institute of Technology-KTH , Department of Applied Physics, Experimental Biomolecular Physics Group, AlbaNova, 106 91 Stockholm, Sweden
| | - Jerker Widengren
- Royal Institute of Technology-KTH , Department of Applied Physics, Experimental Biomolecular Physics Group, AlbaNova, 106 91 Stockholm, Sweden
| | - Lars Tjernberg
- Karolinska Institutet , Department of NVS, Center for Alzheimer Research, Division for Neurogeriatrics, Novum plan 5, 141 86 Stockholm, Sweden
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7
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Gupta B, Mai K, Lowe SB, Wakefield D, Di Girolamo N, Gaus K, Reece PJ, Gooding JJ. Ultrasensitive and Specific Measurement of Protease Activity Using Functionalized Photonic Crystals. Anal Chem 2015; 87:9946-53. [DOI: 10.1021/acs.analchem.5b02529] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Bakul Gupta
- School
of Chemistry, The Australian Centre for NanoMedicine and ARC Centre
of Excellence in Convergent Bio-Nano Science and Technology, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Kelly Mai
- School
of Medical Sciences, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Stuart B. Lowe
- School
of Chemistry, The Australian Centre for NanoMedicine and ARC Centre
of Excellence in Convergent Bio-Nano Science and Technology, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Denis Wakefield
- School
of Medical Sciences, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Nick Di Girolamo
- School
of Medical Sciences, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Katharina Gaus
- EMBL
Australia Node in Single Molecule Science, School of Medical Sciences
and ARC Centre of Excellence in Advanced Molecular Imaging, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Peter J. Reece
- School
of Physics, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - J. Justin Gooding
- School
of Chemistry, The Australian Centre for NanoMedicine and ARC Centre
of Excellence in Convergent Bio-Nano Science and Technology, UNSW Australia, Sydney, New South Wales 2052, Australia
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8
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9
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Zhou C, Li W, Chen J, Yang M, Li Y, Zhu J, Yu C. Real-time fluorometric turn-on assay for protease activity and inhibitor screening with a benzoperylene probe. Analyst 2014; 139:1057-62. [DOI: 10.1039/c3an01724a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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10
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Ridgeway WK, Millar DP, Williamson JR. Vectorized data acquisition and fast triple-correlation integrals for Fluorescence Triple Correlation Spectroscopy. COMPUTER PHYSICS COMMUNICATIONS 2013; 184:1322-1332. [PMID: 23525193 PMCID: PMC3601675 DOI: 10.1016/j.cpc.2012.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fluorescence Correlation Spectroscopy (FCS) is widely used to quantitate reaction rates and concentrations of molecules in vitro and in vivo. We recently reported Fluorescence Triple Correlation Spectroscopy (F3CS), which correlates three signals together instead of two. F3CS can analyze the stoichiometries of complex mixtures and detect irreversible processes by identifying time-reversal asymmetries. Here we report the computational developments that were required for the realization of F3CS and present the results as the Triple Correlation Toolbox suite of programs. Triple Correlation Toolbox is a complete data analysis pipeline capable of acquiring, correlating and fitting large data sets. Each segment of the pipeline handles error estimates for accurate error-weighted global fitting. Data acquisition was accelerated with a combination of off-the-shelf counter-timer chips and vectorized operations on 128-bit registers. This allows desktop computers with inexpensive data acquisition cards to acquire hours of multiple-channel data with sub-microsecond time resolution. Off-line correlation integrals were implemented as a two delay time multiple-tau scheme that scales efficiently with multiple processors and provides an unprecedented view of linked dynamics. Global fitting routines are provided to fit FCS and F3CS data to models containing up to ten species. Triple Correlation Toolbox is a complete package that enables F3CS to be performed on existing microscopes.
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Affiliation(s)
- William K Ridgeway
- Dept. of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037, USA
- Dept. of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037, USA
| | - David P Millar
- Dept. of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037, USA
| | - James R Williamson
- Dept. of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037, USA
- Dept. of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037, USA
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11
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Felekyan S, Sanabria H, Kalinin S, Kühnemuth R, Seidel CAM. Analyzing Förster resonance energy transfer with fluctuation algorithms. Methods Enzymol 2013; 519:39-85. [PMID: 23280107 DOI: 10.1016/b978-0-12-405539-1.00002-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) in combination with Förster resonance energy transfer (FRET) has been developed to a powerful statistical tool, which allows for the analysis of FRET fluctuations in the huge time of nanoseconds to seconds. FRET-FCS utilizes the strong distance dependence of the FRET efficiency on the donor (D)-acceptor (A) distance so that it developed to a perfect method for studying structural fluctuation in biomolecules involved in conformational flexibility, structural dynamics, complex formation, folding, and catalysis. Structural fluctuations thereby result in anticorrelated donor and acceptor signals, which are analyzed by FRET-FCS in order to characterize underlying structural dynamics. Simulated and experimental examples are discussed. First, we review experimental implementations of FRET-FCS and present theory for a two-state interconverting system. Additionally, we consider a very common case of FRET dynamics in the presence of donor-only labeled species. We demonstrate that the mean relaxation time for the structural dynamics can be easily obtained in most of cases, whereas extracting meaningful information from correlation amplitudes can be challenging. We present a strategy to avoid a fit with an underdetermined model function by restraining the D and A brightnesses of the at least one involved state, so that both FRET efficiencies and both rate constants (i.e., the equilibrium constant) can be determined. For samples containing several fluorescent species, the use of pulsed polarized excitation with multiparameter fluorescence detection allows for filtered FCS (fFCS), where species-specific correlation functions can be obtained, which can be directly interpreted. The species selection is achieved by filtering using fluorescence decays of individual species. Analytical functions for species auto- and cross-correlation functions are given. Moreover, fFCS is less affected by photophysical artifacts and often offers higher contrast, which effectively increases its time resolution and significantly enhances its capability to resolve multistate kinetics. fFCS can also differentiate between species even when their brightnesses are the same and thus opens up new possibilities to characterize complex dynamics. Alternative fluctuation algorithms to study FRET dynamics are also briefly reviewed.
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Affiliation(s)
- Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Düsseldorf, Germany
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12
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Blades ML, Grekova E, Wobma HM, Chen K, Chan WCW, Cramb DT. Three-Color Fluorescence Cross-Correlation Spectroscopy for Analyzing Complex Nanoparticle Mixtures. Anal Chem 2012; 84:9623-31. [DOI: 10.1021/ac302572k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Megan L. Blades
- Department of Chemistry, University of Calgary, 2500 University Drive NW, T3A
0J1, Calgary, Alberta, Canada
| | - Ekaterina Grekova
- Department of Chemistry, University of Calgary, 2500 University Drive NW, T3A
0J1, Calgary, Alberta, Canada
| | - Holly M. Wobma
- Department of Chemistry, University of Calgary, 2500 University Drive NW, T3A
0J1, Calgary, Alberta, Canada
| | - Kun Chen
- Institute of Biomaterials and
Biomedical Engineering, Donnelly Centre for Cellular and Biomolecular
Research, Chemistry, Materials Science and Engineering, and Chemical
Engineering, University of Toronto, 160
College Street, Toronto, Ontario, Canada M5S 3E1
| | - Warren C. W. Chan
- Institute of Biomaterials and
Biomedical Engineering, Donnelly Centre for Cellular and Biomolecular
Research, Chemistry, Materials Science and Engineering, and Chemical
Engineering, University of Toronto, 160
College Street, Toronto, Ontario, Canada M5S 3E1
| | - David T. Cramb
- Department of Chemistry, University of Calgary, 2500 University Drive NW, T3A
0J1, Calgary, Alberta, Canada
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14
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Sahoo H. Förster resonance energy transfer – A spectroscopic nanoruler: Principle and applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2011. [DOI: 10.1016/j.jphotochemrev.2011.05.001] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Sahoo H, Schwille P. FRET and FCS--friends or foes? Chemphyschem 2011; 12:532-41. [PMID: 21308943 DOI: 10.1002/cphc.201000776] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 01/07/2011] [Indexed: 11/05/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) are both scientific concepts that are frequently discussed in the context of single-molecule fluorescence techniques. In contrast to FCS, FRET is strictly not a technique but a photophysical phenomenon, which can be employed in combination with any method that probes fluorescence intensity or lifetime. Thus, the combination of FCS with FRET is possible and—although these concepts are quite often treated as alternative approaches, particularly for the analysis of biological systems—also quite attractive. However, under certain circumstances, for example, for applications of fluorescence cross-correlation spectroscopy, FRET effects can cause significant complications for quantitative data analysis, and careful calibration has to be carried out to avoid FRET-induced artifacts. This can be most elegantly done if alternating excitation schemes such as PIE (pulsed interleaved excitation) are employed. In this minireview, we discuss the potential and the caveats of FCS combined with FRET and give a short record on successful and promising applications.
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Affiliation(s)
- Harekrushna Sahoo
- Department of Biophysics, Biotechnologisches Zentrum, Technische Universität Dresden, Tatzberg 47-49, Dresden 01307, Germany
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16
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Ishii K, Tahara T. Resolving inhomogeneity using lifetime-weighted fluorescence correlation spectroscopy. J Phys Chem B 2010; 114:12383-91. [PMID: 20812709 DOI: 10.1021/jp104234c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) was extended by incorporating information of the fluorescence lifetime. This new experimental approach, called lifetime-weighted FCS, enables us to observe fluorescence lifetime fluctuations in the nano- to millisecond time region. The potential of this method for resolving inhomogeneity in complex systems was demonstrated. First, by measuring a mixture of two dye molecules having different fluorescence lifetimes, it was shown that the lifetime-weighted correlation deviates from the ordinary intensity correlation only when the system is inhomogeneous. This demonstrated that lifetime-weighted FCS is capable of detecting inhomogeneity in an ensemble-averaged fluorescence decay profile without any a priori knowledge about the system. Second, we applied this method to a dye-labeled polypeptide, a prototypical model of complex biopolymers. It was found that the ratio between the lifetime-weighted and ordinary intensity correlation changes with change of the environment around the polypeptide. This result was interpreted in terms of environment-dependent conformational inhomogeneity of the polypeptide. Delay time dependence of the ratio was found to be constant from ∼1 μs to several milliseconds, indicating that the observed inhomogeneity is persistent in the measured time scale. In combination with fluorescence intensity correlation, lifetime-weighted FCS allows us to examine conformational fluctuations of complex systems in the time region from nano- to milliseconds, being free from the translational diffusion signal.
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Affiliation(s)
- Kunihiko Ishii
- Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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17
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Loumaigne M, Praho R, Nutarelli D, Werts MHV, Débarre A. Fluorescence correlation spectroscopy reveals strong fluorescence quenching of FITC adducts on PEGylated gold nanoparticles in water and the presence of fluorescent aggregates of desorbed thiolate ligands. Phys Chem Chem Phys 2010; 12:11004-14. [PMID: 20668732 DOI: 10.1039/c004167j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Colloidal gold particles functionalised with oligoethylene-glycolated disulfide ligands and fluorescent moieties derived from fluorescein isothiocyanate (FITC) have been prepared and studied in aqueous suspension using fluorescence correlation spectroscopy (FCS). FCS probes the dynamics of the particles at the single object level, and reveals the desorption of fluorescent ligands which subsequently aggregate into larger (slower diffusing) objects. Cross-correlation spectroscopy of the FITC fluorescence and the Rayleigh-Mie scattering (RM-FCCS) of the gold cores shows that the only detectable fluorescent objects are free ligands and aggregates not associated with a gold particle. The fluorescence of bound fluorophores is quenched making their fluorescence too weak to be detected. FCS and RM-FCCS are useful tools for characterising functionalised noble metal particles in solution, under conditions similar to those used in optical bio-imaging. Desorption of thiolates from gold nanoparticles needs to be taken into account when working with these materials at low concentration.
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Affiliation(s)
- Matthieu Loumaigne
- CNRS, Laboratoire Aimé Cotton (UPR 3321), Université Paris Sud, Bâtiment 505, F-91405 Orsay, France
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18
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Price ES, DeVore MS, Johnson CK. Detecting intramolecular dynamics and multiple Förster resonance energy transfer states by fluorescence correlation spectroscopy. J Phys Chem B 2010; 114:5895-902. [PMID: 20392129 DOI: 10.1021/jp912125z] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a robust method for the detection of intramolecular dynamics in proteins but is also susceptible to interference from other dynamic processes such as triplet kinetics and photobleaching. We describe an approach for the detection of intramolecular dynamics in proteins labeled with a FRET dye pair based on global fitting to the two autocorrelation functions (green-green and red-red) and the two cross-correlation functions (green-red and red-green). We applied the method to detect intramolecular dynamics in the Ca(2+) signaling protein calmodulin. Dynamics were detected on the 100 mus time scale in Ca(2+)-activated calmodulin, whereas in apocalmodulin dynamics were not detected on this time scale. Control measurements on a polyproline FRET construct (Gly-Pro(15)-Cys) demonstrate the reliability of the method for isolating intramolecular dynamics from other dynamic processes on the microsecond time scale and confirm the absence of intramolecular dynamics of polyproline. We further show the sensitivity of the initial amplitudes of the FCS auto- and cross-correlation functions to the presence of multiple FRET states, static or dynamic. The FCS measurements also show that the diffusion of Ca(2+)-calmodulin is slower than that of apocalmodulin, indicating either a larger average hydrodynamic radius or shape effects resulting in a slower translational diffusion.
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Affiliation(s)
- E Shane Price
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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Hillger F, Hänni D, Nettels D, Geister S, Grandin M, Textor M, Schuler B. Probing protein-chaperone interactions with single-molecule fluorescence spectroscopy. Angew Chem Int Ed Engl 2008; 47:6184-8. [PMID: 18618555 DOI: 10.1002/anie.200800298] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Frank Hillger
- Universität Zürich, Biochemisches Institut, 8057 Zürich, Switzerland
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20
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Hillger F, Hänni D, Nettels D, Geister S, Grandin M, Textor M, Schuler B. Untersuchung von Protein-Chaperon-Wechselwirkungen mit Einzelmolekülspektroskopie. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Previte MJR, Pelet S, Kim KH, Buehler C, So PTC. Spectrally resolved fluorescence correlation spectroscopy based on global analysis. Anal Chem 2008; 80:3277-84. [PMID: 18351754 PMCID: PMC5780552 DOI: 10.1021/ac702474u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multicolor fluorescence correlation spectroscopy has been recently developed to study chemical interactions of multiple chemical species labeled with spectrally distinct fluorophores. In the presence of spectral overlap, there exists a lower detectability limit for reaction products with multicolor fluorophores. In addition, the ability to separate bound product from reactants allows thermodynamic properties such as dissociation constants to be measured for chemical reactions. In this report, we utilize a spectrally resolved two-photon microscope with single-photon counting sensitivity to acquire spectral and temporal information from multiple chemical species. Further, we have developed a global fitting analysis algorithm that simultaneously analyzes all distinct auto- and cross-correlation functions from 15 independent spectral channels. We have demonstrated that the global analysis approach allows the concentration and diffusion coefficients of fluorescent particles to be resolved despite the presence of overlapping emission spectra.
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Affiliation(s)
- Michael J R Previte
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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22
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Mahmoud KA, Hrapovic S, Luong JHT. Picomolar detection of protease using peptide/single walled carbon nanotube/gold nanoparticle-modified electrode. ACS NANO 2008; 2:1051-1057. [PMID: 19206503 DOI: 10.1021/nn8000774] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Picomolar electrochemical detection of human immunodeficiency virus type-1 protease (HIV-1 PR) using ferrocene (Fc)-pepstatin-modified surfaces has been presented. Gold electrode surface was modified with gold nanoparticles (AuNP) or thiolated single walled carbon nanotubes/gold nanoparticles (SWCNT/AuNP). Thiol-terminated Fc-pepstatin was then self-assembled on such surfaces as confirmed by Raman spectroscopy and scanning electron microscope. The interaction between the Fc-pepstatin-modified substrates and HIV-1 PR was studied by cyclic voltammetry and electrochemical impedance spectroscopy. Both electrode materials showed enhanced electrochemical responses to increasing concentrations of HIV-1 PR with shifting to higher potentials as well as decrease in the overall signal intensity. However, the sensing electrode modified with thiolated SWCNTs/AuNPs showed remarkable detection sensitivity with an estimated detection limit of 0.8 pM.
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Affiliation(s)
- Khaled A Mahmoud
- Biotechnology Research Institute, National Research Council Canada, Montreal, Canada H4P2R2
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23
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Petrásek Z, Schwille P. Photobleaching in two-photon scanning fluorescence correlation spectroscopy. Chemphyschem 2008; 9:147-58. [PMID: 18072191 DOI: 10.1002/cphc.200700579] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Two-photon excitation in fluorescence correlation spectroscopy (FCS) is often preferred to one-photon excitation because of reduced bulk photobleaching and photodamage, and deeper penetration into scattering media, such as thick biological specimens. Two-photon FCS, however, suffers from lower signal-to-noise ratios which are directly related to the lower molecular brightness achieved. We compare standard FCS with a fixed measurement volume with scanning FCS, where the measurement volume is scanned along a circular path. The experimental results show that photobleaching is the dominant cause of the effects observed at the high excitation powers necessary for good signal-to-noise ratios. Theoretical calculations assuming a nonuniform excitation intensity profile, and using the concept of generalized volume contrast, provide an explanation for the photobleaching effects commonly observed in two-photon FCS at high excitation intensities, without having to assume optical saturation. Scanning alleviates these effects by spreading the photobleaching dose over a larger area, thereby reducing the depletion of fluorescent molecules in the measurement volume. These results, which facilitate understanding of the photobleaching in FCS and of the positive effects of scanning, are particularly important in studies involving the autocorrelation amplitude g(0), such as concentration measurements or binding studies using fluorescence cross-correlation between two labeled species.
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Affiliation(s)
- Zdenek Petrásek
- Biophysics Group, Biotechnologisches Zentrum, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany.
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24
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Nettels D, Hoffmann A, Schuler B. Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds. J Phys Chem B 2008; 112:6137-46. [DOI: 10.1021/jp076971j] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Nettels
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Armin Hoffmann
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Benjamin Schuler
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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Ringemann C, Schönle A, Giske A, von Middendorff C, Hell SW, Eggeling C. Enhancing Fluorescence Brightness: Effect of Reverse Intersystem Crossing Studied by Fluorescence Fluctuation Spectroscopy. Chemphyschem 2008; 9:612-24. [DOI: 10.1002/cphc.200700596] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Kilian KA, Böcking T, Gaus K, Gal M, Gooding JJ. Peptide-modified optical filters for detecting protease activity. ACS NANO 2007; 1:355-361. [PMID: 19206687 DOI: 10.1021/nn700141n] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The organic derivatization of silicon-based nanoporous photonic crystals is presented as a method to immobilize peptides for the detection of protease enzymes in solution. A narrow-line-width rugate filter, a one-dimensional photonic crystal, is fabricated that exhibits a high-reflectivity optical resonance that is sensitive to small changes in the refractive index at the pore walls. To immobilize peptide in the pore of the photonic crystal, the hydrogen-terminated silicon surface was first modified with the alkene 10-succinimidyl undecenoate via hydrosilylation. The monolayer with the succinimide ester moiety at the distal end served the dual function of protecting the underlying silicon from oxidation as well as providing a surface suitable for subsequent derivatization with amines. The surface was further modified with 1-aminohexa(ethylene glycol) (EG(6)) to resist nonspecific adsorption of proteins common in complex biological samples. The distal hydroxyl of the EG(6) is activated using the solid-phase coupling reagent disuccinimidyl carbonate for selective immobilization of peptides as protease recognition elements. X-ray photoelectron spectroscopy analysis reveals high activation and coupling efficiency at each stage of the functionalization. Exposure of the peptide-modified crystals to the protease subtilisin in solution causes a change in the refractive index, resulting in a shift of the resonance to shorter wavelengths, indicating cleavage of organic material within the pores. The lowest detected concentration of enzyme was 37 nM (7.4 pmol in 200 microL).
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Affiliation(s)
- Kristopher A Kilian
- School of Chemistry, Centre for Vascular Research, University of New South Wales, Sydney NSW 2052, Australia
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27
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Haustein E, Schwille P. Fluorescence correlation spectroscopy: novel variations of an established technique. ACTA ACUST UNITED AC 2007; 36:151-69. [PMID: 17477838 DOI: 10.1146/annurev.biophys.36.040306.132612] [Citation(s) in RCA: 372] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is one of the major biophysical techniques used for unraveling molecular interactions in vitro and in vivo. It allows minimally invasive study of dynamic processes in biological specimens with extremely high temporal and spatial resolution. By recording and correlating the fluorescence fluctuations of single labeled molecules through the exciting laser beam, FCS gives information on molecular mobility and photophysical and photochemical reactions. By using dual-color fluorescence cross-correlation, highly specific binding studies can be performed. These have been extended to four reaction partners accessible by multicolor applications. Alternative detection schemes shift accessible time frames to slower processes (e.g., scanning FCS) or higher concentrations (e.g., TIR-FCS). Despite its long tradition, FCS is by no means dated. Rather, it has proven to be a highly versatile technique that can easily be adapted to solve specific biological questions, and it continues to find exciting applications in biology and medicine.
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Affiliation(s)
- Elke Haustein
- BioTec TU Dresden, Institute for Biophysics, D-01307 Dresden, Germany.
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28
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Hwang LC, Wohland T. Recent Advances in Fluorescence Cross-correlation Spectroscopy. Cell Biochem Biophys 2007; 49:1-13. [PMID: 17873335 DOI: 10.1007/s12013-007-0042-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 11/30/1999] [Accepted: 05/21/2007] [Indexed: 12/14/2022]
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is a method that measures the temporal fluorescence fluctuations coming from two differently labeled molecules diffusing through a small sample volume. Cross-correlation analysis of the fluorescence signals from separate detection channels extracts information of the dynamics of the dual-labeled molecules. FCCS has become an essential tool for the characterization of diffusion coefficients, binding constants, kinetic rates of binding, and determining molecular interactions in solutions and cells. By cross-correlating between two focal spots, flow properties could also be measured. Recent developments in FCCS have been targeted at using different experimental schemes to improve on the sensitivity and address their limitations such as cross-talk and alignment issues. This review presents an overview of the different excitation and detection methodologies used in FCCS and their biological applications. This is followed by a description of the fluorescent probes currently available for the different methods. This will introduce biological readers to FCCS and its related techniques and provide a starting point to selecting which experimental scheme is suitable for their type of biological study.
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Affiliation(s)
- Ling Chin Hwang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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29
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Eggeling C, Widengren J, Brand L, Schaffer J, Felekyan S, Seidel CAM. Analysis of photobleaching in single-molecule multicolor excitation and Förster resonance energy transfer measurements. J Phys Chem A 2007; 110:2979-95. [PMID: 16509620 DOI: 10.1021/jp054581w] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dye photobleaching is a major constraint of fluorescence readout within a range of applications. In this study, we investigated the influence of photobleaching in fluorescence experiments applying multicolor laser as well as Förster resonance energy transfer (FRET) mediated excitation using several red-emitting dyes frequently used in multicolor experiments or as FRET acceptors. The chosen dyes (cyanine 5 (Cy5), MR121, Alexa660, Alexa680, Atto647N, Atto655) have chemically distinct chromophore systems and can be excited at 650 nm. Several fluorescence analysis techniques have been applied to detect photobleaching and to disclose the underlying photophysics, all of which are based on single-molecule detection: (1) fluorescence correlation spectroscopy (FCS) of bulk solutions, (2) fluorescence cross-correlation of single-molecule trajectories, and (3) multiparameter fluorescence detection (MFD) of single-molecule events. The maximum achievable fluorescence signals as well as the survival times of the red dyes were markedly reduced under additional laser irradiation in the range of 500 nm. Particularly at excitation levels at or close to saturation, the 500 nm irradiation effectively induced transitions to higher excited electronic states on already excited dye molecules, leading to a pronounced bleaching reactivity. A theoretical model for the observed laser irradiance dependence of the fluorescence brightness of a Cy5 FRET acceptor dye has been developed introducing the full description of the underlying photophysics. The model takes into account acceptor as well as donor photobleaching from higher excited electronic states, population of triplet states, and energy transfer to both the ground and excited states of the acceptor dye. Also, photoinduced reverse intersystem crossing via higher excited triplet states is included, which was found to be very efficient for Cy5 attached to DNA. Comparing continuous wave (cw) and pulsed donor excitation, a strong enhancement of acceptor photobleaching by a factor of 5 was observed for the latter. Thus, in the case of fluorescence experiments utilizing multicolor pulsed laser excitation, the application of the appropriate timing of synchronized green and red laser pulses in an alternating excitation mode can circumvent excessive photobleaching. Moreover, important new single-molecule analysis diagnosis tools are presented: (1) For the case of excessive acceptor photobleaching, cross-correlation analysis of single-molecule trajectories of the fluorescence signal detected in the donor and acceptor detection channels and vice versa shows an anticorrelated exponential decay and growth, respectively. (2) The time difference, Tg - Tr, of the mean observation times of all photons detected for the donor and acceptor detection channels within a single-molecule fluorescence burst allows one to identify and exclude molecules with an event of acceptor photobleaching. The presented single-molecule analysis methods can be constrained to, for example, FRET-active subpopulations, reducing bias from FRET-inactive molecules. The observations made are of strong relevance for and demand a careful choice of laser action in multicolor and FRET experiments, in particular when performed at or close to saturation.
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Affiliation(s)
- Christian Eggeling
- Department of NanoBiophotonics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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30
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Huebsch ND, Mooney DJ. Fluorescent resonance energy transfer: A tool for probing molecular cell-biomaterial interactions in three dimensions. Biomaterials 2007; 28:2424-37. [PMID: 17270268 PMCID: PMC2176075 DOI: 10.1016/j.biomaterials.2007.01.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Accepted: 01/04/2007] [Indexed: 12/11/2022]
Abstract
The current paradigm in designing biomaterials is to optimize material chemical and physical parameters based on correlations between these parameters and downstream biological responses, whether in vitro or in vivo. Extensive developments in molecular design of biomaterials have facilitated identification of several biophysical and biochemical variables (e.g. adhesion peptide density, substrate elastic modulus) as being critical to cell response. However, these empirical observations do not indicate whether different parameters elicit cell responses by modulating redundant variables of the cell-material interface (e.g. number of cell-material bonds, cell-matrix mechanics). Recently, fluorescence resonance energy transfer (FRET) has been applied to quantitatively analyze parameters of the cell-material interface for both two- and three-dimensional adhesion substrates. Tools based on FRET have been utilized to quantify several parameters of the cell-material interface relevant to cell response, including molecular changes in matrix proteins induced by interactions both with surfaces and cells, the number of bonds between integrins and their adhesion ligands, and changes in the crosslink density of hydrogel synthetic extracellular matrix analogs. As such techniques allow both dynamic and 3-D analyses they will be useful to quantitatively relate downstream cellular responses (e.g. gene expression) to the composition of this interface. Such understanding will allow bioengineers to fully exploit the potential of biomaterials engineered on the molecular scale, by optimizing material chemical and physical properties to a measurable set of interfacial parameters known to elicit a predictable response in a specific cell population. This will facilitate the rational design of complex, multi-functional biomaterials used as model systems for studying diseases or for clinical applications.
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Affiliation(s)
- Nathaniel D Huebsch
- Division of Engineering and Applied Sciences, Harvard University, USA; Harvard-MIT Division of Health Sciences and Technology, USA
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31
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Satsoura D, Leber B, Andrews DW, Fradin C. Circumvention of fluorophore photobleaching in fluorescence fluctuation experiments: a beam scanning approach. Chemphyschem 2007; 8:834-48. [PMID: 17394281 PMCID: PMC2891014 DOI: 10.1002/cphc.200600589] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2006] [Indexed: 12/31/2022]
Abstract
Photobleaching is a fluorophore-damaging process that commonly afflicts single-molecule fluorescence studies. It becomes an especially severe problem in fluorescence fluctuation experiments when studying slowly diffusing particles. One way to circumvent this problem is to use beam scanning to decrease the residence time of the fluorophores in the excitation volume. We report a systematic study of the effects of circular beam scanning on the photobleaching of fluorescent particles as observed in single-photon excitation fluorescence fluctuation experiments. We start by deriving a simple expression relating the average detected fluorescence to the photobleaching cross section of the fluorophores. We then perform numerical calculations of the spatial distribution of fluorescent particles in order to understand under which conditions beam scanning can prevent the formation of a photobleaching hole. To support these predictions, we show experimental results obtained for large unilamellar vesicles containing a small amount of the fluorescent lipophilic tracer DiD. We establish the required scanning radius and frequency range in order to obtain sufficient reduction of the photobleaching effect for that system. From the detected increase in fluorescence upon increase in scanning speed, we estimate the photobleaching cross section of DiD.
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Affiliation(s)
- Dmitri Satsoura
- D. Satsoura, Dr. B. Leber, Dr. D. W. Andrews, Dr. C. Fradin, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON, L8N3Z5 (Canada)
| | - Brian Leber
- D. Satsoura, Dr. B. Leber, Dr. D. W. Andrews, Dr. C. Fradin, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON, L8N3Z5 (Canada)
| | - David W. Andrews
- D. Satsoura, Dr. B. Leber, Dr. D. W. Andrews, Dr. C. Fradin, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON, L8N3Z5 (Canada)
| | - Cécile Fradin
- Dr. C. Fradin, Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, L8S4M1 (Canada), Fax: (+1) 905-546-1252,
- D. Satsoura, Dr. B. Leber, Dr. D. W. Andrews, Dr. C. Fradin, Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, ON, L8N3Z5 (Canada)
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Marks BD, Qadir N, Eliason HC, Shekhani MS, Doering K, Vogel KW. Multiparameter analysis of a screen for progesterone receptor ligands: comparing fluorescence lifetime and fluorescence polarization measurements. Assay Drug Dev Technol 2006; 3:613-22. [PMID: 16438657 DOI: 10.1089/adt.2005.3.613] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Direct measurement of the fluorescence lifetime (FLT) of a fluorescent label is an emerging method for high-throughput screening. Changes in the fluorescence lifetime can be correlated to changes in the non-radiative relaxation pathway(s) for the excited state of the label. These pathways can be environmentally sensitive, such as when a labeled analyte is free in solution versus bound to a receptor. Because lifetime is an intrinsic property of a fluorophore, it is not concentration dependent, and therefore has advantages similar to those of ratiometric fluorescent techniques such as fluorescence resonance energy transfer or fluorescence polarization. We have applied the FLT measurement technique to a screen of a small compound library in order to identify compounds that bind to the progesterone receptor, and compared the results to those obtained by performing the assay in fluorescence polarization mode. Each readout modality showed excellent Z'; values, with the FLT readout performing slightly better in this respect. Interfering compounds could be rapidly identified for either assay format by comparing the results between the two formats.
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Johnson CK. Calmodulin, conformational states, and calcium signaling. A single-molecule perspective. Biochemistry 2006; 45:14233-46. [PMID: 17128963 PMCID: PMC2533622 DOI: 10.1021/bi061058e] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule fluorescence measurements can provide a new perspective on the conformations, dynamics, and interactions of proteins. Recent examples are described illustrating the application of single-molecule fluorescence spectroscopy to calcium signaling proteins with an emphasis on the new information available in single-molecule fluorescence burst measurements, resonance energy transfer, and polarization modulation methods. Calcium signaling pathways are crucial in many cellular processes. The calcium binding protein calmodulin (CaM) serves as a molecular switch to regulate a network of calcium signaling pathways. Single-molecule spectroscopic methods can yield insights into conformations and dynamics of CaM and CaM-regulated proteins. Examples include studies of the conformations and dynamics of CaM, binding of target peptides, and interaction with the plasma-membrane Ca2+ pump. Single-molecule resonance energy transfer measurements revealed conformational substates of CaM, and single-molecule polarization modulation spectroscopy was used to probe interactions between CaM and the plasma-membrane Ca2+-ATPase.
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Affiliation(s)
- Carey K Johnson
- Department of Chemistry, 1251 Wescoe Drive, University of Kansas, Lawrence, Kansas 66045-7582, USA.
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34
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Hwang LC, Gösch M, Lasser T, Wohland T. Simultaneous multicolor fluorescence cross-correlation spectroscopy to detect higher order molecular interactions using single wavelength laser excitation. Biophys J 2006; 91:715-27. [PMID: 16632502 PMCID: PMC1483109 DOI: 10.1529/biophysj.105.074120] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 04/05/2006] [Indexed: 11/18/2022] Open
Abstract
Fluorescence cross-correlation spectroscopy is a powerful method for the study of molecular interactions and dynamics in solution and even in living cells. Usually, in the optical setup, either two laser beams have to be superimposed in their respective confocal volumes or two-photon excitation is used for a dual-color detection system. It has been shown recently that fluorescence cross correlation can be achieved with spectrally similar fluorophores using single wavelength excitation fluorescence cross-correlation spectroscopy (SW-FCCS). In this study, we show that SW-FCCS allows the simultaneous excitation of up to three fluorophores in which the cross correlation of their fluctuation signals is detected separately in three detection channels. The experimental and theoretical model to describe triple pairwise cross correlations incorporating cross talk and possible changes in emission characteristics such as quenching upon binding are outlined. The effectiveness of SW-FCCS to detect binding of three interacting partners is experimentally verified with a standard ligand-receptor model, biotin-streptavidin, where differently labeled biotin ligands and their binding to a third-color labeled streptavidin are studied. The cross-correlation amplitudes and their changes with stoichiometric binding are analyzed and the upper limits of dissociation constants are determined. Performed with appropriate negative controls, SW-FCCS can determine interaction patterns between ligands and receptors.
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Affiliation(s)
- Ling Chin Hwang
- National University of Singapore, Department of Chemistry, Singapore 117543, Singapore
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35
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Olofsson M, Kalinin S, Zdunek J, Oliveberg M, Johansson LBA. Tryptophan-BODIPY: a versatile donor-acceptor pair for probing generic changes of intraprotein distances. Phys Chem Chem Phys 2006; 8:3130-40. [PMID: 16804615 DOI: 10.1039/b601313a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that Tryptophan (Trp) and N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-yl)methyl iodoacetamide (BODIPY) is a suitable donor-acceptor (D-A) pair for intraprotein distance measurements, applicable to the study of protein folding. The suitability of the Trp-BODIPY electronic energy transfer is exemplified on the extensively-characterised two-state protein, S6, from Thermus thermophilus. This protein has proved to be useful for the elucidation of folding cooperativity and nucleation, as well as the changes upon induction of structural transitions. For a comprehensive structural coverage, BODIPY molecules were anchored by Cys insertions at four different positions on the S6 surface. Trp residues at position 33 or 62 acted as donors of electronic energy to the BODIPY groups. None of the D-A pairs show any detectable difference in the folding kinetics (or protein stability), which supports the notion that the two-state transition of S6 is a highly concerted process. Similar results are obtained for mutants affecting the N- and C-terminus. The kinetic analyses indicate that changes of the transition state occur through local unfolding of the native state, rather than by a decrease of the folding cooperativity. The distances obtained from the analysis of the time-resolved fluorescence experiments in the native state were compared to those calculated from X-ray structure. As an additional measure, molecular dynamics simulations of the different protein constructs were performed to account for variability in the BODIPY location on the protein surface. The agreement between fluorescence and X-ray data is quite convincing, and shows that energy transfer measurements between Trp and BODIPY can probe distances between ca. 17 to 34 A, with an error better than 10%.
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Affiliation(s)
- Maria Olofsson
- Biophysical Chemistry and Biochemistry, Department of Chemistry, Umeå University, S-901 87 Umeå, Sweden
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36
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Swift JL, Heuff R, Cramb DT. A two-photon excitation fluorescence cross-correlation assay for a model ligand-receptor binding system using quantum dots. Biophys J 2006; 90:1396-410. [PMID: 16299079 PMCID: PMC1367290 DOI: 10.1529/biophysj.105.069526] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 10/27/2005] [Indexed: 11/18/2022] Open
Abstract
Two-photon excitation fluorescence cross-correlation spectroscopy (TPE-XCS) is a very suitable method for studying interactions of two distinctly labeled fluorescent molecules. As such, it lends itself nicely to the study of ligand-receptor interactions. By labeling the ligand with one color of fluorescent dye and the receptor with another, it is possible to directly monitor ligand binding rather than inferring binding by monitoring downstream effects. One challenge of the TPE-XCS approach is that of separating the signal due to the receptor from that of the ligand. Using standard organic fluorescent labels there is almost inevitably spectral cross talk between the detection channels, which must be accounted for in TPE-XCS data analysis. However, using quantum dots as labels for both ligand and receptor this limitation can be alleviated, because of the dot's narrower emission spectra. Using solely quantum dots as fluorescent labels is a novel approach to TPE-XCS, which may be generalizable to many pairs of interacting biomolecules after the proof of principle and the assessment of limitations presented here. Moreover, it is essential that relevant pharmacological parameters such as the equilibrium dissociation constant, K(d), can be easily extracted from the XCS data with minimal processing. Herein, we present a modified expression for fractional occupancy based on the auto- and cross-correlation decays obtained from a well-defined ligand-receptor system. Nanocrystalline semiconductor quantum dots functionalized with biotin (lambda(em) = 605 nm) and streptavidin (lambda(em) = 525 nm) were used for which an average K(d) value of 0.30 +/- 0.04 x 10(-9) M was obtained (cf. native system approximately 10(-15)). Additionally, the off-rate coefficient (k(off)) for dissociation of the two quantum dots was determined as 5 x 10(-5) s(-1). This off-rate is slightly larger than for native biotin-streptavidin (5 x 10(-6) s(-1)); the bulky nature of the quantum dots and restricted motion/orientation of functionalized dots in solution can account for differences in the streptavidin-biotin mediated dot-dot binding compared with those for native streptavidin-biotin.
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Affiliation(s)
- J L Swift
- Department of Chemistry, University of Calgary, Calgary AB, T2N 1N4, Canada
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