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Kay TM, Aplin CP, Simonet R, Beenken J, Miller RC, Libal C, Boersma AJ, Sheets ED, Heikal AA. Molecular Brightness Approach for FRET Analysis of Donor-Linker-Acceptor Constructs at the Single Molecule Level: A Concept. Front Mol Biosci 2021; 8:730394. [PMID: 34595208 PMCID: PMC8476790 DOI: 10.3389/fmolb.2021.730394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In this report, we have developed a simple approach using single-detector fluorescence autocorrelation spectroscopy (FCS) to investigate the Förster resonance energy transfer (FRET) of genetically encoded, freely diffusing crTC2.1 (mTurquoise2.1-linker-mCitrine) at the single molecule level. We hypothesize that the molecular brightness of the freely diffusing donor (mTurquoise2.1) in the presence of the acceptor (mCitrine) is lower than that of the donor alone due to FRET. To test this hypothesis, the fluorescence fluctuation signal and number of molecules of freely diffusing construct were measured using FCS to calculate the molecular brightness of the donor, excited at 405 nm and detected at 475/50 nm, in the presence and absence of the acceptor. Our results indicate that the molecular brightness of cleaved crTC2.1 in a buffer is larger than that of the intact counterpart under 405-nm excitation. The energy transfer efficiency at the single molecule level is larger and more spread in values as compared with the ensemble-averaging time-resolved fluorescence measurements. In contrast, the molecular brightness of the intact crTC2.1, under 488 nm excitation of the acceptor (531/40 nm detection), is the same or slightly larger than that of the cleaved counterpart. These FCS-FRET measurements on freely diffusing donor-acceptor pairs are independent of the precise time constants associated with autocorrelation curves due to the presence of potential photophysical processes. Ultimately, when used in living cells, the proposed approach would only require a low expression level of these genetically encoded constructs, helping to limit potential interference with the cell machinery.
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Affiliation(s)
- Taryn M Kay
- Department of Physics and Astronomy, University of Minnesota Duluth, Duluth, MN, United States
| | - Cody P Aplin
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Rowan Simonet
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Julie Beenken
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Robert C Miller
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Christin Libal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Arnold J Boersma
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
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Hossain SS, Paul S, Samanta A. Structural Stability and Conformational Dynamics of Cytochrome c in Hydrated Deep Eutectic Solvents. J Phys Chem B 2021; 125:5757-5765. [PMID: 34042450 DOI: 10.1021/acs.jpcb.1c01975] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many deep eutectic solvents (DESs) are currently being explored as environment-friendly media for biorelated applications. As an understanding of the effect of these solvents on the structure of biomolecules is crucial for these applications, we study how two DESs comprising trimethylglycine (TMG) and ethylene glycol (EG) or glycerol (GL) influence the structural stability and conformational dynamics of cytochrome c (Cytc) using single-molecule-based fluorescence correlation spectroscopy (FCS) technique and several other ensemble-based biophysical methods. The FCS studies on A488-labeled Cytc enable an estimation of the size (20.5 ± 1.5 Å) of the protein and capture its conformational dynamics (54 ± 2 μs) in aqueous buffered solution. It is observed that both size and conformational dynamics of the protein are influenced in the presence of the DESs, but this effect is more pronounced in the case of TMG-EG. The ensemble measurements on both labeled and wild-type Cytc reveal that the protein structure is unfolded completely by TMG-EG, whereas the structure is slightly altered by TMG-GL. The results suggest that the behavior of Cytc in hydrated DESs is determined by the strength of interactions between the DES constituents as well as that between the constituents and the water molecules present in the system.
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Affiliation(s)
- Sk Saddam Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sneha Paul
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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3
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Perez-Gonzalez DC, Penedo JC. Single-Molecule Strategies for DNA and RNA Diagnostics. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Ishii K, Tahara T. Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. 2. Application. J Phys Chem B 2013; 117:11423-32. [DOI: 10.1021/jp406864e] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Kügel W, Muschielok A, Michaelis J. Bayesian-inference-based fluorescence correlation spectroscopy and single-molecule burst analysis reveal the influence of dye selection on DNA hairpin dynamics. Chemphyschem 2012; 13:1013-22. [PMID: 22279001 DOI: 10.1002/cphc.201100720] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Indexed: 01/30/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) is a powerful tool to gain information about dynamics of biomolecules. However, the key problem is to extract the rates hidden in the FCS data by fitting the data to a meaningful model. A number of different fitting approaches have been described in recent years but the extraction of relevant information to date has still been limited by numerous experimental problems and the fact that the set of starting parameter values chosen could often predefine the result. We establish a new way to globally analyze FCS data based on Bayesian inference to overcome these issues. Moreover, the influence of other remaining experimental error sources, for example, photophysics, is excluded by additional means. Using this approach in combination with the results from single-molecule burst analysis, we investigate the kinetics of DNA hairpins labeled with a variety of different fluorescent probes as a function of the salt concentration. We find that the rates of hairpin opening and closing as well as the equilibrium constant of the transition depend on the characteristics of the dye molecules used to label the hairpin. Thus, great caution has to be used when utilizing dye molecules as reporters for the kinetics of dynamic macromolecular structures.
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Affiliation(s)
- Wolfgang Kügel
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
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Torella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN. Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis. Biophys J 2011; 100:1568-77. [PMID: 21402040 DOI: 10.1016/j.bpj.2011.01.066] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 12/31/2010] [Accepted: 01/20/2011] [Indexed: 12/22/2022] Open
Abstract
Histograms of single-molecule Förster resonance energy transfer (FRET) efficiency are often used to study the structures of biomolecules and relate these structures to function. Methods like probability distribution analysis analyze FRET histograms to detect heterogeneities in molecular structure, but they cannot determine whether this heterogeneity arises from dynamic processes or from the coexistence of several static structures. To this end, we introduce burst variance analysis (BVA), a method that detects dynamics by comparing the standard deviation of FRET from individual molecules over time to that expected from theory. Both simulations and experiments on DNA hairpins show that BVA can distinguish between static and dynamic sources of heterogeneity in single-molecule FRET histograms and can test models of dynamics against the observed standard deviation information. Using BVA, we analyzed the fingers-closing transition in the Klenow fragment of Escherichia coli DNA polymerase I and identified substantial dynamics in polymerase complexes formed prior to nucleotide incorporation; these dynamics may be important for the fidelity of DNA synthesis. We expect BVA to be broadly applicable to single-molecule FRET studies of molecular structure and to complement approaches such as probability distribution analysis and fluorescence correlation spectroscopy in studying molecular dynamics.
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Affiliation(s)
- Joseph P Torella
- Department of Physics and Biological Physics Research Group, University of Oxford, Oxford, United Kingdom
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Levitus M. Relaxation Kinetics by Fluorescence Correlation Spectroscopy: Determination of Kinetic Parameters in the Presence of Fluorescent Impurities. J Phys Chem Lett 2010; 1:1346-1350. [PMID: 20454591 PMCID: PMC2863333 DOI: 10.1021/jz100231v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The use of Fluorescence Correlation Spectroscopy (FCS) in combination with Förster Resonance Energy Transfer (FRET) is gaining popularity as a tool to investigate kinetics in equilibrium conditions. The technique is based on the study of fluorescence fluctuations in small numbers of molecules, and is particularly well-suited to investigate conformational dynamics in biopolymers. In practice, its applicability is often hindered by the presence of certain impurities such as partially labeled biomolecules, excess of free fluorophore, or partially dissociated multi-subunit complexes. Here, we show that the simultaneous measurement of the fluctuations in the donor and acceptor intensities allows the determination of the kinetic relaxation time of the reaction in the presence of donor-only particles when cross-talk is negligible, or in cases where all species have the same diffusion coefficient. Theoretical predictions are supported with the results of Monte Carlo simulations, and demonstrate that the applicability of the technique is more general than previously thought.
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Affiliation(s)
- Marcia Levitus
- Biodesign Institute and Department of Chemistry and Biochemistry. Arizona State University. PO BOX 876501. Tempe, AZ 85287-5601
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Gurunathan K, Levitus M. FRET fluctuation spectroscopy of diffusing biopolymers: contributions of conformational dynamics and translational diffusion. J Phys Chem B 2010; 114:980-6. [PMID: 20030305 DOI: 10.1021/jp907390n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The use of fluorescence correlation spectroscopy (FCS) to study conformational dynamics in diffusing biopolymers requires that the contributions to the signal due to translational diffusion are separated from those due to conformational dynamics. A simple approach that has been proposed to achieve this goal involves the analysis of fluctuations in fluorescence resonance energy transfer (FRET) efficiency. In this work, we investigate the applicability of this methodology by combining Monte Carlo simulations and experiments. Results show that diffusion does not contribute to the measured fluctuations in FRET efficiency in conditions where the relaxation time of the kinetic process is much shorter than the mean transit time of the molecules in the optical observation volume. However, in contrast to what has been suggested in previous work, the contributions of diffusion are otherwise significant. Neglecting the contributions of diffusion can potentially lead to an erroneous interpretation of the kinetic mechanisms. As an example, we demonstrate that the analysis of FRET fluctuations in terms of a purely kinetic model would generally lead to the conclusion that the system presents complex kinetic behavior even for an idealized two-state system.
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Affiliation(s)
- Kaushik Gurunathan
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5601, USA
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Hansen DF, Feng H, Zhou Z, Bai Y, Kay LE. Selective characterization of microsecond motions in proteins by NMR relaxation. J Am Chem Soc 2009; 131:16257-65. [PMID: 19842628 PMCID: PMC7386800 DOI: 10.1021/ja906842s] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The three-dimensional structures of macromolecules fluctuate over a wide range of time-scales. Separating the individual dynamic processes according to frequency is of importance in relating protein motions to biological function and stability. We present here a general NMR method for the specific characterization of microsecond motions at backbone positions in proteins even in the presence of other dynamics such as large-amplitude nanosecond motions and millisecond chemical exchange processes. The method is based on measurement of relaxation rates of four bilinear coherences and relies on the ability of strong continuous radio frequency fields to quench millisecond chemical exchange. The utility of the methodology is demonstrated and validated through two specific examples focusing on the thermo-stable proteins, ubiquitin and protein L, where it is found that small-amplitude microsecond dynamics are more pervasive than previously thought. Specifically, these motions are localized to alpha helices, loop regions, and regions along the rim of beta sheets in both of the proteins examined. A third example focuses on a 28 kDa ternary complex of the chaperone Chz1 and the histones H2A.Z/H2B, where it is established that pervasive microsecond motions are localized to a region of the chaperone that is important for stabilizing the complex. It is further shown that these motions can be well separated from extensive millisecond dynamics that are also present and that derive from exchange of Chz1 between bound and free states. The methodology is straightforward to implement, and data recorded at only a single static magnetic field are required.
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Affiliation(s)
- D Flemming Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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