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Gopich IV, Chung HS. Unraveling Burst Selection Bias in Single-Molecule FRET of Species with Unequal Brightness and Diffusivity. J Phys Chem B 2024; 128:5576-5589. [PMID: 38833567 DOI: 10.1021/acs.jpcb.4c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Single-molecule free diffusion experiments enable accurate quantification of coexisting species or states. However, unequal brightness and diffusivity introduce a burst selection bias and affect the interpretation of experimental results. We address this issue with a photon-by-photon maximum likelihood method, burstML, which explicitly considers burst selection criteria. BurstML accurately estimates parameters, including photon count rates, diffusion times, Förster resonance energy transfer (FRET) efficiencies, and population, even in cases where species are poorly distinguished in FRET efficiency histograms. We develop a quantitative theory that determines the fraction of photon bursts corresponding to each species and thus obtain accurate species populations from the measured burst fractions. In addition, we provide a simple approximate formula for burst fractions and establish the range of parameters where unequal brightness and diffusivity can significantly affect the results obtained by conventional methods. The performance of the burstML method is compared with that of a maximum likelihood method that assumes equal species brightness and diffusivity, as well as standard Gaussian fitting of FRET efficiency histograms, using both simulated and real single-molecule data for cold-shock protein, protein L, and protein G. The burstML method enhances the accuracy of parameter estimation in single-molecule fluorescence studies.
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Affiliation(s)
- Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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2
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Liu Z, Liu H, Vera AM, Yang B, Tinnefeld P, Nash MA. Engineering an artificial catch bond using mechanical anisotropy. Nat Commun 2024; 15:3019. [PMID: 38589360 PMCID: PMC11001878 DOI: 10.1038/s41467-024-46858-9] [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: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Catch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociate the complex using five precisely controlled anchor geometries. When tension is applied between residue #13 on CohE and the N-terminus of DocG, the complex behaves as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaves as a slip bond. We use a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrate that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Department of Bionanoscience, Delft University of Technology, 2629HZ, Delft, the Netherlands
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland.
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
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3
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Prindle JR, de Cuba OIC, Gahlmann A. Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects. J Chem Phys 2023; 159:071002. [PMID: 37589409 PMCID: PMC10908566 DOI: 10.1063/5.0155638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/06/2023] [Indexed: 08/18/2023] Open
Abstract
Most biological processes in living cells rely on interactions between proteins. Live-cell compatible approaches that can quantify to what extent a given protein participates in homo- and hetero-oligomeric complexes of different size and subunit composition are therefore critical to advance our understanding of how cellular physiology is governed by these molecular interactions. Biomolecular complex formation changes the diffusion coefficient of constituent proteins, and these changes can be measured using fluorescence microscopy-based approaches, such as single-molecule tracking, fluorescence correlation spectroscopy, and fluorescence recovery after photobleaching. In this review, we focus on the use of single-molecule tracking to identify, resolve, and quantify the presence of freely-diffusing proteins and protein complexes in living cells. We compare and contrast different data analysis methods that are currently employed in the field and discuss experimental designs that can aid the interpretation of the obtained results. Comparisons of diffusion rates for different proteins and protein complexes in intracellular aqueous environments reported in the recent literature reveal a clear and systematic deviation from the Stokes-Einstein diffusion theory. While a complete and quantitative theoretical explanation of why such deviations manifest is missing, the available data suggest the possibility of weighing freely-diffusing proteins and protein complexes in living cells by measuring their diffusion coefficients. Mapping individual diffusive states to protein complexes of defined molecular weight, subunit stoichiometry, and structure promises to provide key new insights into how protein-protein interactions regulate protein conformational, translational, and rotational dynamics, and ultimately protein function.
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Affiliation(s)
- Joshua Robert Prindle
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Olivia Isabella Christiane de Cuba
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, USA
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4
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Coñuecar R, Asela I, Rivera M, Galaz-Davison P, González-Higueras J, Hamilton GL, Engelberger F, Ramírez-Sarmiento CA, Babul J, Sanabria H, Medina E. DNA facilitates heterodimerization between human transcription factors FoxP1 and FoxP2 by increasing their conformational flexibility. iScience 2023; 26:107228. [PMID: 37485372 PMCID: PMC10362293 DOI: 10.1016/j.isci.2023.107228] [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: 10/03/2022] [Revised: 05/15/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Transcription factors regulate gene expression by binding to DNA. They have disordered regions and specific DNA-binding domains. Binding to DNA causes structural changes, including folding and interactions with other molecules. The FoxP subfamily of transcription factors in humans is unique because they can form heterotypic interactions without DNA. However, it is unclear how they form heterodimers and how DNA binding affects their function. We used computational and experimental methods to study the structural changes in FoxP1's DNA-binding domain when it forms a heterodimer with FoxP2. We found that FoxP1 has complex and diverse conformational dynamics, transitioning between compact and extended states. Surprisingly, DNA binding increases the flexibility of FoxP1, contrary to the typical folding-upon-binding mechanism. In addition, we observed a 3-fold increase in the rate of heterodimerization after FoxP1 binds to DNA. These findings emphasize the importance of structural flexibility in promoting heterodimerization to form transcriptional complexes.
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Affiliation(s)
- Ricardo Coñuecar
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Isabel Asela
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - George L. Hamilton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Felipe Engelberger
- Institute for Drug Discovery, Leipzig University Medical School, 04107 Leipzig, Germany
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- ANID – Millennium Science Initiative Program – Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
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5
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Harris PD, Lerner E. Identification and quantification of within-burst dynamics in singly labeled single-molecule fluorescence lifetime experiments. BIOPHYSICAL REPORTS 2022; 2. [PMID: 36204594 PMCID: PMC9534301 DOI: 10.1016/j.bpr.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Single-molecule spectroscopy has revolutionized molecular biophysics and provided means to probe how structural moieties within biomolecules spatially reorganize at different timescales. There are several single-molecule methodologies that probe local structural dynamics in the vicinity of a single dye-labeled residue, which rely on fluorescence lifetimes as readout. Nevertheless, an analytical framework to quantify dynamics in such single-molecule single dye fluorescence bursts, at timescales of microseconds to milliseconds, has not yet been demonstrated. Here, we suggest an analytical framework for identifying and quantifying within-burst lifetime-based dynamics, such as conformational dynamics recorded in single-molecule photo-isomerization-related fluorescence enhancement. After testing the capabilities of the analysis on simulations, we proceed to exhibit within-burst millisecond local structural dynamics in the unbound α-synuclein monomer. The analytical framework provided in this work paves the way for extracting a full picture of the energy landscape for the coordinate probed by fluorescence lifetime-based single-molecule measurements.
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Affiliation(s)
- Paul David Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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6
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Abstract
Single molecule Förster resonance energy transfer (smFRET) is a unique biophysical approach for studying conformational dynamics in biomacromolecules. Photon-by-photon hidden Markov modeling (H2MM) is an analysis tool that can quantify FRET dynamics of single biomolecules, even if they occur on the sub-millisecond timescale. However, dye photophysical transitions intertwined with FRET dynamics may cause artifacts. Here, we introduce multi-parameter H2MM (mpH2MM), which assists in identifying FRET dynamics based on simultaneous observation of multiple experimentally-derived parameters. We show the importance of using mpH2MM to decouple FRET dynamics caused by conformational changes from photophysical transitions in confocal-based smFRET measurements of a DNA hairpin, the maltose binding protein, MalE, and the type-III secretion system effector, YopO, from Yersinia species, all exhibiting conformational dynamics ranging from the sub-second to microsecond timescales. Overall, we show that using mpH2MM facilitates the identification and quantification of biomolecular sub-populations and their origin. In this work, the authors demonstrate the application of multi-parameter photon-by-photon hidden Markov modeling (mpH2MM) on alternating laser excitation (ALEX)-based smFRET measurements. The utility of mpH2MM in identifying and quantifying dynamic biomolecular sub-populations is demonstrated in three different systems.
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7
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Vera AM, Galera-Prat A, Wojciechowski M, Różycki B, Laurents DV, Carrión-Vázquez M, Cieplak M, Tinnefeld P. Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization. Structure 2021; 29:587-597.e8. [PMID: 33561387 DOI: 10.1016/j.str.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule fluorescence resonance energy transfer and molecular simulations on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.
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Affiliation(s)
- Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Albert Galera-Prat
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | | | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
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8
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Sanders JC, Holmstrom ED. Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins. Essays Biochem 2021; 65:37-49. [PMID: 33600559 PMCID: PMC8052285 DOI: 10.1042/ebc20200022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/17/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022]
Abstract
The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole-dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered).
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Affiliation(s)
- Joshua C Sanders
- Department of Chemistry, University of Kansas, Lawrence, KS, U.S.A
| | - Erik D Holmstrom
- Department of Chemistry, University of Kansas, Lawrence, KS, U.S.A
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, U.S.A
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9
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Vink JNA, Brouns SJJ, Hohlbein J. Extracting Transition Rates in Particle Tracking Using Analytical Diffusion Distribution Analysis. Biophys J 2020; 119:1970-1983. [PMID: 33086040 DOI: 10.1016/j.bpj.2020.09.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/29/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022] Open
Abstract
Single-particle tracking is an important technique in the life sciences to understand the kinetics of biomolecules. The analysis of apparent diffusion coefficients in vivo, for example, enables researchers to determine whether biomolecules are moving alone, as part of a larger complex, or are bound to large cellular components such as the membrane or chromosomal DNA. A remaining challenge has been to retrieve quantitative kinetic models, especially for molecules that rapidly switch between different diffusional states. Here, we present analytical diffusion distribution analysis (anaDDA), a framework that allows for extracting transition rates from distributions of apparent diffusion coefficients calculated from short trajectories that feature less than 10 localizations per track. Under the assumption that the system is Markovian and diffusion is purely Brownian, we show that theoretically predicted distributions accurately match simulated distributions and that anaDDA outperforms existing methods to retrieve kinetics, especially in the fast regime of 0.1-10 transitions per imaging frame. AnaDDA does account for the effects of confinement and tracking window boundaries. Furthermore, we added the option to perform global fitting of data acquired at different frame times to allow complex models with multiple states to be fitted confidently. Previously, we have started to develop anaDDA to investigate the target search of CRISPR-Cas complexes. In this work, we have optimized the algorithms and reanalyzed experimental data of DNA polymerase I diffusing in live Escherichia coli. We found that long-lived DNA interaction by DNA polymerase are more abundant upon DNA damage, suggesting roles in DNA repair. We further revealed and quantified fast DNA probing interactions that last shorter than 10 ms. AnaDDA pushes the boundaries of the timescale of interactions that can be probed with single-particle tracking and is a mathematically rigorous framework that can be further expanded to extract detailed information about the behavior of biomolecules in living cells.
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Affiliation(s)
- Jochem N A Vink
- Department of Bionanoscience, Delft University of Technology, HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, the Netherlands; Microspectroscopy Reasearch Facility, Wageningen University & Research, Wageningen, the Netherlands.
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10
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Medina E, Villalobos P, Hamilton GL, Komives EA, Sanabria H, Ramírez-Sarmiento CA, Babul J. Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping. J Mol Biol 2020; 432:5411-5429. [PMID: 32735805 DOI: 10.1016/j.jmb.2020.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/01/2023]
Abstract
Forkhead box P (FoxP) proteins are unique transcription factors that spatiotemporally regulate gene expression by tethering two chromosome loci together via functional domain-swapped dimers formed through their DNA-binding domains. Further, the differential kinetics on this dimerization mechanism underlie an intricate gene regulation network at physiological conditions. Nonetheless, poor understanding of the structural dynamics and steps of the association process impedes to link the functional domain swapping to human-associated diseases. Here, we have characterized the DNA-binding domain of human FoxP1 by integrating single-molecule Förster resonance energy transfer and hydrogen-deuterium exchange mass spectrometry data with molecular dynamics simulations. Our results confirm the formation of a previously postulated domain-swapped (DS) FoxP1 dimer in solution and reveal the presence of highly populated, heterogeneous, and locally disordered dimeric intermediates along the dimer dissociation pathway. The unique features of FoxP1 provide a glimpse of how intrinsically disordered regions can facilitate domain swapping oligomerization and other tightly regulated association mechanisms relevant in biological processes.
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Affiliation(s)
- Exequiel Medina
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Pablo Villalobos
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - George L Hamilton
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Elizabeth A Komives
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Hugo Sanabria
- Department of Physics & Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | - Jorge Babul
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile.
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11
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Vink JNA, Martens KJA, Vlot M, McKenzie RE, Almendros C, Estrada Bonilla B, Brocken DJW, Hohlbein J, Brouns SJJ. Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism. Mol Cell 2020; 77:39-50.e10. [PMID: 31735642 DOI: 10.1016/j.molcel.2019.10.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/31/2019] [Accepted: 10/11/2019] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here, we visualize individual Cascade complexes in a native type I CRISPR-Cas system. We uncover an exponential relation between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and affect CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.
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Affiliation(s)
- Jochem N A Vink
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Koen J A Martens
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Laboratory of Bionanotechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands
| | - Rebecca E McKenzie
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Cristóbal Almendros
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Boris Estrada Bonilla
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daan J W Brocken
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, the Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands; Microspectroscopy Research Facility, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands.
| | - Stan J J Brouns
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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12
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Mazal H, Haran G. Single-molecule FRET methods to study the dynamics of proteins at work. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019; 12:8-17. [PMID: 31989063 PMCID: PMC6984960 DOI: 10.1016/j.cobme.2019.08.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Feynman commented that "Everything that living things do can be understood in terms of the jiggling and wiggling of atoms". Proteins can jiggle and wiggle large structural elements such as domains and subunits as part of their functional cycles. Single-molecule fluorescence resonance energy transfer (smFRET) is an excellent tool to study conformational dynamics and decipher coordinated large-scale motions within proteins. smFRET methods introduced in recent years are geared toward understanding the time scales and amplitudes of function-related motions. This review discusses the methodology for obtaining and analyzing smFRET temporal trajectories that provide direct dynamic information on transitions between conformational states. It also introduces correlation methods that are useful for characterizing intramolecular motions. This arsenal of techniques has been used to study multiple molecular systems, from membrane proteins through molecular chaperones, and we examine some of these studies here. Recent exciting methodological novelties permit revealing very fast, submillisecond dynamics, whose relevance to protein function is yet to be fully grasped.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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13
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Quast RB, Margeat E. Studying GPCR conformational dynamics by single molecule fluorescence. Mol Cell Endocrinol 2019; 493:110469. [PMID: 31163201 DOI: 10.1016/j.mce.2019.110469] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023]
Abstract
Over the last decades, G protein coupled receptors (GPCRs) have experienced a tremendous amount of attention, which has led to a boost of structural and pharmacological insights on this large membrane protein superfamily involved in various essential physiological functions. Recently, evidence has emerged that, rather than being activated by ligands in an on/off manner switching from an inactive to an active state, GPCRs exhibit high structural flexibility in the absence and even in the presence of ligands. So far the physiological as well as pharmacological impact of this structural flexibility remains largely unexplored albeit its potential role in precisely fine-tuning receptor function and regulating the specificity of signal transduction into the cell. By complementing other biophysical approaches, single molecule fluorescence (SMF) offers the advantage of monitoring structural dynamics in biomolecules in real-time, with minimal structural invasiveness and in the context of complex biological environments. In this review a general introduction to GPCR structural dynamics is given followed by a presentation of SMF methods used to explore them. Particular attention is paid to single molecule Förster resonance energy transfer (smFRET), a key method to measure actual distance changes between two probes, and highlight conformational changes occurring at timescales relevant for protein conformational movements. The available literature reporting on GPCR structural dynamics by SMF is discussed with a focus on the newly gained biological insights on receptor activation and signaling, in particular for the β2 adrenergic and the metabotropic glutamate receptors.
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Affiliation(s)
- Robert B Quast
- CBS, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Emmanuel Margeat
- CBS, CNRS, INSERM, Université de Montpellier, Montpellier, France.
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14
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Barth A, Voith von Voithenberg L, Lamb DC. Quantitative Single-Molecule Three-Color Förster Resonance Energy Transfer by Photon Distribution Analysis. J Phys Chem B 2019; 123:6901-6916. [PMID: 31117611 DOI: 10.1021/acs.jpcb.9b02967] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Single-molecule Förster resonance energy transfer (FRET) is a powerful tool to study conformational dynamics of biomolecules. Using solution-based single-pair FRET by burst analysis, conformational heterogeneities and fluctuations of fluorescently labeled proteins or nucleic acids can be studied by monitoring a single distance at a time. Three-color FRET is sensitive to three distances simultaneously and can thus elucidate complex coordinated motions within single molecules. While three-color FRET has been applied on the single-molecule level before, a detailed quantitative description of the obtained FRET efficiency distributions is still missing. Direct interpretation of three-color FRET data is additionally complicated by an increased shot noise contribution when converting photon counts to FRET efficiencies. However, to address the question of coordinated motion, it is of special interest to extract information about the underlying distance heterogeneity, which is not easily extracted from the FRET efficiency histograms directly. Here, we present three-color photon distribution analysis (3C-PDA), a method to extract distributions of interdye distances from three-color FRET measurements. We present a model for diffusion-based three-color FRET experiments and apply Bayesian inference to extract information about the physically relevant distance heterogeneity in the sample. The approach is verified using simulated data sets and experimentally applied to triple-labeled DNA duplexes. Finally, three-color FRET experiments on the Hsp70 chaperone BiP reveal conformational coordinated changes between individual domains. The possibility to address the co-occurrence of intramolecular distances makes 3C-PDA a powerful method to study the coordination of domain motions within biomolecules undergoing conformational dynamics.
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Affiliation(s)
- Anders Barth
- Department of Chemistry, Center for Integrated Protein Science Munich, Nanosystems Initiative Munich and Center for Nanoscience , Ludwig-Maximilians-Universität München , Butenandtstr. 5-13 , 81377 Munich , Germany
| | - Lena Voith von Voithenberg
- Department of Chemistry, Center for Integrated Protein Science Munich, Nanosystems Initiative Munich and Center for Nanoscience , Ludwig-Maximilians-Universität München , Butenandtstr. 5-13 , 81377 Munich , Germany
| | - Don C Lamb
- Department of Chemistry, Center for Integrated Protein Science Munich, Nanosystems Initiative Munich and Center for Nanoscience , Ludwig-Maximilians-Universität München , Butenandtstr. 5-13 , 81377 Munich , Germany
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15
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Okamoto K, Sako Y. Single-Molecule Förster Resonance Energy Transfer Measurement Reveals the Dynamic Partially Ordered Structure of the Epidermal Growth Factor Receptor C-Tail Domain. J Phys Chem B 2019; 123:571-581. [PMID: 30571124 DOI: 10.1021/acs.jpcb.8b10066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered proteins (IDPs) or regions (IDRs) are thought to exhibit unique functionalities without forming ordered structures. However, these molecular mechanisms are not easily elucidated, partly because of the difficultly of measuring structural information. In this study, we applied the alternative laser excitation (ALEX) method and circular dichroism (CD) spectroscopy to investigate the structure of the C-terminal tail (CTT) domain of the human epidermal growth factor receptor (EGFR). The single-molecule distributions of Förster resonance energy transfer (FRET) obtained by ALEX under solution conditions modified by the addition of potassium chloride (KCl), urea, or guanidinium chloride (GdmCl) allowed us to separately examine the influences of charge interactions and secondary structure formation. The CD spectrum analyses indicated the types of included secondary structure. The results suggested that the structure of the CTT is influenced by secondary structure formation, which is a principally antiparallel β-sheet, rather than by charge interactions and that phosphorylation of the major Grb2-binding sites partially denatures that secondary structure. Our findings suggest that the EGFR CTT might regulate ligand binding kinetics by local β-sheet formation or by the disruption associated with phosphorylation states.
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Affiliation(s)
- Kenji Okamoto
- Cellular Informatics Laboratory , RIKEN , 2-1 Hirosawa , Wako , Saitama 351-0198 Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory , RIKEN , 2-1 Hirosawa , Wako , Saitama 351-0198 Japan
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16
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Vandenberk N, Karamanou S, Portaliou AG, Zorzini V, Hofkens J, Hendrix J, Economou A. The Preprotein Binding Domain of SecA Displays Intrinsic Rotational Dynamics. Structure 2018; 27:90-101.e6. [PMID: 30471924 DOI: 10.1016/j.str.2018.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/27/2018] [Accepted: 10/10/2018] [Indexed: 11/26/2022]
Abstract
SecA converts ATP energy to protein translocation work. Together with the membrane-embedded SecY channel it forms the bacterial protein translocase. How secretory proteins bind to SecA and drive conformational cascades to promote their secretion remains unknown. To address this, we focus on the preprotein binding domain (PBD) of SecA. PBD crystalizes in three distinct states, swiveling around its narrow stem. Here, we examined whether PBD displays intrinsic dynamics in solution using single-molecule Förster resonance energy transfer (smFRET). Unique cysteinyl pairs on PBD and apposed domains were labeled with donor/acceptor dyes. Derivatives were analyzed using pulsed interleaved excitation and multi-parameter fluorescence detection. The PBD undergoes significant rotational motions, occupying at least three distinct states in dimeric and four in monomeric soluble SecA. Nucleotides do not affect smFRET-detectable PBD dynamics. These findings lay the foundations for single-molecule dissection of translocase mechanics and suggest models for possible PBD involvement during catalysis.
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Affiliation(s)
- Niels Vandenberk
- KU Leuven, Department of Chemistry, Division for Molecular Imaging and Photonics, Laboratory for Photochemistry and Spectroscopy, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Spyridoula Karamanou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Athina G Portaliou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Valentina Zorzini
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium
| | - Johan Hofkens
- KU Leuven, Department of Chemistry, Division for Molecular Imaging and Photonics, Laboratory for Photochemistry and Spectroscopy, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Jelle Hendrix
- KU Leuven, Department of Chemistry, Division for Molecular Imaging and Photonics, Laboratory for Photochemistry and Spectroscopy, Celestijnenlaan 200F, B-3001 Leuven, Belgium; Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, B-3590 Diepenbeek, Belgium.
| | - Anastassios Economou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Molecular Bacteriology, Herestraat 49, Gasthuisberg Campus, B-3000 Leuven, Belgium.
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17
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Vandenberk N, Barth A, Borrenberghs D, Hofkens J, Hendrix J. Evaluation of Blue and Far-Red Dye Pairs in Single-Molecule Förster Resonance Energy Transfer Experiments. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Niels Vandenberk
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science, Nanosystems Initiative Munich and Centre for Nanoscience, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Agoralaan C (BIOMED), Diepenbeek, B-3590, Belgium
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18
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Talavera A, Hendrix J, Versées W, Jurėnas D, Van Nerom K, Vandenberk N, Singh RK, Konijnenberg A, De Gieter S, Castro-Roa D, Barth A, De Greve H, Sobott F, Hofkens J, Zenkin N, Loris R, Garcia-Pino A. Phosphorylation decelerates conformational dynamics in bacterial translation elongation factors. SCIENCE ADVANCES 2018; 4:eaap9714. [PMID: 29546243 PMCID: PMC5851678 DOI: 10.1126/sciadv.aap9714] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Bacterial protein synthesis is intricately connected to metabolic rate. One of the ways in which bacteria respond to environmental stress is through posttranslational modifications of translation factors. Translation elongation factor Tu (EF-Tu) is methylated and phosphorylated in response to nutrient starvation upon entering stationary phase, and its phosphorylation is a crucial step in the pathway toward sporulation. We analyze how phosphorylation leads to inactivation of Escherichia coli EF-Tu. We provide structural and biophysical evidence that phosphorylation of EF-Tu at T382 acts as an efficient switch that turns off protein synthesis by decoupling nucleotide binding from the EF-Tu conformational cycle. Direct modifications of the EF-Tu switch I region or modifications in other regions stabilizing the β-hairpin state of switch I result in an effective allosteric trap that restricts the normal dynamics of EF-Tu and enables the evasion of the control exerted by nucleotides on G proteins. These results highlight stabilization of a phosphorylation-induced conformational trap as an essential mechanism for phosphoregulation of bacterial translation and metabolism. We propose that this mechanism may lead to the multisite phosphorylation state observed during dormancy and stationary phase.
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Affiliation(s)
- Ariel Talavera
- Structural Biology Brussels, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Structural Biology, VIB, Flanders, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics, University of Leuven, B-3001 Leuven, Belgium
- Biomedical Research Institute, Hasselt University, B-3590 Hasselt, Belgium
| | - Wim Versées
- Structural Biology Brussels, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Structural Biology, VIB, Flanders, Belgium
| | - Dukas Jurėnas
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
| | - Niels Vandenberk
- Molecular Imaging and Photonics, University of Leuven, B-3001 Leuven, Belgium
| | - Ranjan Kumar Singh
- Structural Biology Brussels, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Structural Biology, VIB, Flanders, Belgium
| | - Albert Konijnenberg
- Structural Biology Brussels, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Structural Biology, VIB, Flanders, Belgium
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Steven De Gieter
- Structural Biology Brussels, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Structural Biology, VIB, Flanders, Belgium
| | - Daniel Castro-Roa
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Anders Barth
- Fluorescence Applications in Biology Laboratory, Department of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Henri De Greve
- Structural Biology Brussels, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Structural Biology, VIB, Flanders, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Johan Hofkens
- Molecular Imaging and Photonics, University of Leuven, B-3001 Leuven, Belgium
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Remy Loris
- Structural Biology Brussels, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Structural Biology, VIB, Flanders, Belgium
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, Brussels, Belgium
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19
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Peulen TO, Opanasyuk O, Seidel CAM. Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately. J Phys Chem B 2017; 121:8211-8241. [PMID: 28709377 PMCID: PMC5592652 DOI: 10.1021/acs.jpcb.7b03441] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Förster resonance energy transfer
(FRET) measurements from
a donor, D, to an acceptor, A, fluorophore are frequently used in vitro and in live cells to reveal information on the
structure and dynamics of DA labeled macromolecules. Accurate descriptions
of FRET measurements by molecular models are complicated because the
fluorophores are usually coupled to the macromolecule via flexible
long linkers allowing for diffusional exchange between multiple states
with different fluorescence properties caused by distinct environmental
quenching, dye mobilities, and variable DA distances. It is often
assumed for the analysis of fluorescence intensity decays that DA
distances and D quenching are uncorrelated (homogeneous quenching
by FRET) and that the exchange between distinct fluorophore states
is slow (quasistatic). This allows us to introduce the FRET-induced
donor decay, εD(t), a function solely
depending on the species fraction distribution of the rate constants
of energy transfer by FRET, for a convenient joint analysis of fluorescence
decays of FRET and reference samples by integrated graphical and analytical
procedures. Additionally, we developed a simulation toolkit to model
dye diffusion, fluorescence quenching by the protein surface, and
FRET. A benchmark study with simulated fluorescence decays of 500
protein structures demonstrates that the quasistatic homogeneous model
works very well and recovers for single conformations the average
DA distances with an accuracy of < 2%. For more complex
cases, where proteins adopt multiple conformations with significantly
different dye environments (heterogeneous case), we introduce a general
analysis framework and evaluate its power in resolving heterogeneities
in DA distances. The developed fast simulation methods, relying on
Brownian dynamics of a coarse-grained dye in its sterically accessible
volume, allow us to incorporate structural information in the decay
analysis for heterogeneous cases by relating dye states with protein
conformations to pave the way for fluorescence and FRET-based dynamic
structural biology. Finally, we present theories and simulations to
assess the accuracy and precision of steady-state and time-resolved
FRET measurements in resolving DA distances on the single-molecule
and ensemble level and provide a rigorous framework for estimating
approximation, systematic, and statistical errors.
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Affiliation(s)
- Thomas-Otavio Peulen
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Oleg Opanasyuk
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität , Universitätsstraße 1, 40225 Düsseldorf, Germany
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20
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Benke S, Nettels D, Hofmann H, Schuler B. Quantifying kinetics from time series of single-molecule Förster resonance energy transfer efficiency histograms. NANOTECHNOLOGY 2017; 28:114002. [PMID: 28103588 DOI: 10.1088/1361-6528/aa5abd] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Single-molecule fluorescence spectroscopy is a powerful approach for probing biomolecular structure and dynamics, including protein folding. For the investigation of nonequilibrium kinetics, Förster resonance energy transfer combined with confocal multiparameter detection has proven particularly versatile, owing to the large number of observables and the broad range of accessible timescales, especially in combination with rapid microfluidic mixing. However, a comprehensive kinetic analysis of the resulting time series of transfer efficiency histograms and complementary observables can be challenging owing to the complexity of the data. Here we present and compare three different methods for the analysis of such kinetic data: singular value decomposition, multivariate curve resolution with alternating least square fitting, and model-based peak fitting, where an explicit model of both the transfer efficiency histogram of each species and the kinetic mechanism of the process is employed. While each of these methods has its merits for specific applications, we conclude that model-based peak fitting is most suitable for a quantitative analysis and comparison of kinetic mechanisms.
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Affiliation(s)
- Stephan Benke
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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21
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Hohlbein J, Kapanidis AN. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET. Methods Enzymol 2016; 581:353-378. [PMID: 27793286 DOI: 10.1016/bs.mie.2016.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open and closed conformations of DNA polymerases, our smFRET assays utilizing doubly labeled variants of Escherichia coli DNA polymerase I were pivotal in identifying and characterizing a partially closed conformation as a primary checkpoint for nucleotide selection. Here, we provide a comprehensive overview of the methods we used for the conformational analysis of wild-type DNA polymerase and some of its low-fidelity derivatives; these methods include strategies for protein labeling and our procedures for solution-based single-molecule fluorescence data acquisition and data analysis. We also discuss alternative single-molecule fluorescence strategies for analyzing the conformations of DNA polymerases in vitro and in vivo.
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Affiliation(s)
- J Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, The Netherlands; Microspectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands.
| | - A N Kapanidis
- Clarendon Laboratory, University of Oxford, Oxford, United Kingdom.
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22
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Dolino DM, Rezaei Adariani S, Shaikh SA, Jayaraman V, Sanabria H. Conformational Selection and Submillisecond Dynamics of the Ligand-binding Domain of the N-Methyl-d-aspartate Receptor. J Biol Chem 2016; 291:16175-85. [PMID: 27226581 PMCID: PMC4965566 DOI: 10.1074/jbc.m116.721274] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 01/22/2023] Open
Abstract
The N-methyl-d-aspartate (NMDA) receptors are heteromeric non-selective cation channels that require the binding of glycine and glutamate for gating. Based on crystal structures, the mechanism of partial agonism at the glycine-binding site is thought to be mediated by a shift in the conformational equilibrium between an open clamshell and a closed clamshell-like structure of the bilobed ligand-binding domain (LBD). Using single-molecule Förster resonance energy transfer (smFRET) and multiparameter fluorescence detection, which allows us to study the conformational states and dynamics in the submillisecond time scale, we show that there are at least three conformational states explored by the LBD: the low FRET, medium FRET, and high FRET states. The distance of the medium and low FRET states corresponds to what has been observed in crystallography structures. We show that the high FRET state, which would represent a more closed clamshell conformation than that observed in the crystal structure, is most likely the state initiating activation, as evidenced by the fact that the fraction of the protein in this state correlates well with the extent of activation. Furthermore, full agonist bound LBDs show faster dynamic motions between the medium and high FRET states, whereas they show slower dynamics when bound to weaker agonists or to antagonists.
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Affiliation(s)
- Drew M Dolino
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center, Graduate School for Biomedical Sciences, Houston, Texas 77030 and
| | | | - Sana A Shaikh
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center, Graduate School for Biomedical Sciences, Houston, Texas 77030 and
| | - Vasanthi Jayaraman
- From the Department of Biochemistry and Molecular Biology, Center for Membrane Biology, University of Texas Health Science Center, Graduate School for Biomedical Sciences, Houston, Texas 77030 and
| | - Hugo Sanabria
- the Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634
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23
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Characterizing 3D RNA structure by single molecule FRET. Methods 2016; 103:57-67. [PMID: 26853327 DOI: 10.1016/j.ymeth.2016.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/26/2022] Open
Abstract
The importance of elucidating the three dimensional structures of RNA molecules is becoming increasingly clear. However, traditional protein structural techniques such as NMR and X-ray crystallography have several important drawbacks when probing long RNA molecules. Single molecule Förster resonance energy transfer (smFRET) has emerged as a useful alternative as it allows native sequences to be probed in physiological conditions and allows multiple conformations to be probed simultaneously. This review serves to describe the method of generating a three dimensional RNA structure from smFRET data from the biochemical probing of the secondary structure to the computational refinement of the final model.
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24
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Kulesza A, Daly S, MacAleese L, Antoine R, Dugourd P. Structural exploration and Förster theory modeling for the interpretation of gas-phase FRET measurements: Chromophore-grafted amyloid-β peptides. J Chem Phys 2015; 143:025101. [DOI: 10.1063/1.4926390] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Alexander Kulesza
- Institut Lumière Matière, UMR5306 Université Claude Bernard Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
| | - Steven Daly
- Institut Lumière Matière, UMR5306 Université Claude Bernard Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
| | - Luke MacAleese
- Institut Lumière Matière, UMR5306 Université Claude Bernard Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
| | - Rodolphe Antoine
- Institut Lumière Matière, UMR5306 Université Claude Bernard Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
| | - Philippe Dugourd
- Institut Lumière Matière, UMR5306 Université Claude Bernard Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne Cedex, France
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25
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Fine tuning of sub-millisecond conformational dynamics controls metabotropic glutamate receptors agonist efficacy. Nat Commun 2014; 5:5206. [DOI: 10.1038/ncomms6206] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/09/2014] [Indexed: 11/08/2022] Open
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26
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Gust A, Zander A, Gietl A, Holzmeister P, Schulz S, Lalkens B, Tinnefeld P, Grohmann D. A starting point for fluorescence-based single-molecule measurements in biomolecular research. Molecules 2014; 19:15824-65. [PMID: 25271426 PMCID: PMC6271140 DOI: 10.3390/molecules191015824] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.
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Affiliation(s)
- Alexander Gust
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Adrian Zander
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Birka Lalkens
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany.
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27
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Hohlbein J, Craggs TD, Cordes T. Alternating-laser excitation: single-molecule FRET and beyond. Chem Soc Rev 2014; 43:1156-71. [PMID: 24037326 DOI: 10.1039/c3cs60233h] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems.
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Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands.
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28
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Murphy RR, Danezis G, Horrocks MH, Jackson SE, Klenerman D. Bayesian Inference of Accurate Population Sizes and FRET Efficiencies from Single Diffusing Biomolecules. Anal Chem 2014; 86:8603-12. [DOI: 10.1021/ac501188r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rebecca R. Murphy
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - George Danezis
- Department
of Computer Science, University College London, London WC1E 6BT, United Kingdom
| | - Mathew H. Horrocks
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sophie E. Jackson
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - David Klenerman
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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29
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Tsukanov R, Tomov TE, Liber M, Berger Y, Nir E. Developing DNA nanotechnology using single-molecule fluorescence. Acc Chem Res 2014; 47:1789-98. [PMID: 24828396 DOI: 10.1021/ar500027d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and Holliday junctions and of the interactions of DNA strands with DNA origami and origami-related devices such as a DNA bipedal motor are provided. These examples demonstrate how SMF can be utilized for measurement of distances and conformational distributions and equilibrium and nonequilibrium kinetics, to monitor structural integrity and operation of DNA devices, and for isolation and investigation of minor subpopulations including malfunctioning and nonreactive devices. Utilization of a flow-cell to achieve measurements of dynamics with increased time resolution and for convenient and efficient operation of DNA devices is discussed briefly. We conclude by summarizing the various benefits provided by SMF for the development of DNA nanotechnology and suggest that the method can significantly assist in the design and manufacture and evaluation of operation of DNA devices.
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Affiliation(s)
- Roman Tsukanov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Toma E. Tomov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Miran Liber
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Yaron Berger
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Eyal Nir
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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30
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Farooq S, Fijen C, Hohlbein J. Studying DNA-protein interactions with single-molecule Förster resonance energy transfer. PROTOPLASMA 2014; 251:317-32. [PMID: 24374460 DOI: 10.1007/s00709-013-0596-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has emerged as a powerful tool for elucidating biological structure and mechanisms on the molecular level. Here, we focus on applications of smFRET to study interactions between DNA and enzymes such as DNA and RNA polymerases. SmFRET, used as a nanoscopic ruler, allows for the detection and precise characterisation of dynamic and rarely occurring events, which are otherwise averaged out in ensemble-based experiments. In this review, we will highlight some recent developments that provide new means of studying complex biological systems either by combining smFRET with force-based techniques or by using data obtained from smFRET experiments as constrains for computer-aided modelling.
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Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands
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31
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The Power of Single-Molecule FRET Microscopy Applied to DNA Nanotechnology. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-38815-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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32
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Tsukanov R, Tomov TE, Berger Y, Liber M, Nir E. Conformational Dynamics of DNA Hairpins at Millisecond Resolution Obtained from Analysis of Single-Molecule FRET Histograms. J Phys Chem B 2013; 117:16105-9. [DOI: 10.1021/jp411280n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Roman Tsukanov
- Department of Chemistry
and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Toma E. Tomov
- Department of Chemistry
and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Yaron Berger
- Department of Chemistry
and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Miran Liber
- Department of Chemistry
and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Eyal Nir
- Department of Chemistry
and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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33
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DeVore MS, Gull SF, Johnson CK. Reconstruction of Calmodulin Single-Molecule FRET States, Dye-Interactions, and CaMKII Peptide Binding by MultiNest and Classic Maximum Entropy. Chem Phys 2013; 422:10.1016/j.chemphys.2012.11.018. [PMID: 24223465 PMCID: PMC3819237 DOI: 10.1016/j.chemphys.2012.11.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca2+ binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.
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Affiliation(s)
- Matthew S. DeVore
- Department of Chemistry, University of Kansas, Lawrence, Kansas, 66045, United States
| | - Stephen F. Gull
- Astrophysics Group, Department of Physics, Cambridge University, Cambridge CB3 0HE, United Kingdom
| | - Carey K. Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas, 66045, United States
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34
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Rothwell PJ, Allen WJ, Sisamakis E, Kalinin S, Felekyan S, Widengren J, Waksman G, Seidel CAM. dNTP-dependent conformational transitions in the fingers subdomain of Klentaq1 DNA polymerase: insights into the role of the "nucleotide-binding" state. J Biol Chem 2013; 288:13575-91. [PMID: 23525110 DOI: 10.1074/jbc.m112.432690] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Conformational selection plays a key role in the polymerase cycle. RESULTS Klentaq1 exists in conformational equilibrium between three states (open, closed, and “nucleotide-binding”) whose level of occupancy is determined by the bound substrate. CONCLUSION The “nucleotide-binding” state plays a pivotal role in the reaction pathway. SIGNIFICANCE Direct evidence is provided for the role of a conformationally distinct “nucleotide-binding” state during dNTP incorporation. DNA polymerases are responsible for the accurate replication of DNA. Kinetic, single-molecule, and x-ray studies show that multiple conformational states are important for DNA polymerase fidelity. Using high precision FRET measurements, we show that Klentaq1 (the Klenow fragment of Thermus aquaticus DNA polymerase 1) is in equilibrium between three structurally distinct states. In the absence of nucleotide, the enzyme is mostly open, whereas in the presence of DNA and a correctly base-pairing dNTP, it re-equilibrates to a closed state. In the presence of a dNTP alone, with DNA and an incorrect dNTP, or in elevated MgCl2 concentrations, an intermediate state termed the "nucleotide-binding" state predominates. Photon distribution and hidden Markov modeling revealed fast dynamic and slow conformational processes occurring between all three states in a complex energy landscape suggesting a mechanism in which dNTP delivery is mediated by the nucleotide-binding state. After nucleotide binding, correct dNTPs are transported to the closed state, whereas incorrect dNTPs are delivered to the open state.
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Affiliation(s)
- Paul J Rothwell
- Chair for Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstraβe 1, 40225 Düsseldorf, Germany.
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35
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Kalinin S, Peulen T, Sindbert S, Rothwell PJ, Berger S, Restle T, Goody RS, Gohlke H, Seidel CAM. A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nat Methods 2012; 9:1218-25. [PMID: 23142871 DOI: 10.1038/nmeth.2222] [Citation(s) in RCA: 299] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 10/05/2012] [Indexed: 12/17/2022]
Abstract
We present a comprehensive toolkit for Förster resonance energy transfer (FRET)-restrained modeling of biomolecules and their complexes for quantitative applications in structural biology. A dramatic improvement in the precision of FRET-derived structures is achieved by explicitly considering spatial distributions of dye positions, which greatly reduces uncertainties due to flexible dye linkers. The precision and confidence levels of the models are calculated by rigorous error estimation. The accuracy of this approach is demonstrated by docking a DNA primer-template to HIV-1 reverse transcriptase. The derived model agrees with the known X-ray structure with an r.m.s. deviation of 0.5 Å. Furthermore, we introduce FRET-guided 'screening' of a large structural ensemble created by molecular dynamics simulations. We used this hybrid approach to determine the formerly unknown configuration of the flexible single-strand template overhang.
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Affiliation(s)
- Stanislav Kalinin
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität (HHU), Düsseldorf, Germany.
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36
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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.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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37
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DeVore MS, Gull SF, Johnson CK. Classic maximum entropy recovery of the average joint distribution of apparent FRET efficiency and fluorescence photons for single-molecule burst measurements. J Phys Chem B 2012; 116:4006-15. [PMID: 22338694 PMCID: PMC3320690 DOI: 10.1021/jp209861u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We describe a method for analysis of single-molecule Förster resonance energy transfer (FRET) burst measurements using classic maximum entropy. Classic maximum entropy determines the Bayesian inference for the joint probability describing the total fluorescence photons and the apparent FRET efficiency. The method was tested with simulated data and then with DNA labeled with fluorescent dyes. The most probable joint distribution can be marginalized to obtain both the overall distribution of fluorescence photons and the apparent FRET efficiency distribution. This method proves to be ideal for determining the distance distribution of FRET-labeled biomolecules, and it successfully predicts the shape of the recovered distributions.
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Affiliation(s)
- Matthew S. DeVore
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
| | - Stephen F. Gull
- Astrophysics Group, Department of Physics, Cambridge University, Cambridge CB3 0HE, UK
| | - Carey K. Johnson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
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38
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Kudryavtsev V, Sikor M, Kalinin S, Mokranjac D, Seidel CAM, Lamb DC. Combining MFD and PIE for accurate single-pair Förster resonance energy transfer measurements. Chemphyschem 2012; 13:1060-78. [PMID: 22383292 DOI: 10.1002/cphc.201100822] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/30/2011] [Indexed: 12/13/2022]
Abstract
Single-pair Förster resonance energy transfer (spFRET) experiments using single-molecule burst analysis on a confocal microscope are an ideal tool to measure inter- and intramolecular distances and dynamics on the nanoscale. Different techniques have been developed to maximize the amount of information available in spFRET burst analysis experiments. Multiparameter fluorescence detection (MFD) is used to monitor a variety of fluorescence parameters simultaneously and pulsed interleaved excitation (PIE) employs direct excitation of the acceptor to probe its presence and photoactivity. To calculate accurate FRET efficiencies from spFRET experiments with MFD or PIE, several calibration measurements are usually required. Herein, we demonstrate that by combining MFD with PIE information regarding all calibration factors as well as an accurate determination of spFRET histograms can be performed in a single measurement. In addition, the quality of overlap of the different detection volumes as well as the detection of acceptor photophysics can be investigated with MFD-PIE. Bursts containing acceptor photobleaching can be identified and excluded from further investigation while bursts that contain FRET dynamics are unaffected by this analysis. We have employed MFD-PIE to accurately analyze the effects of nucleotides and substrate on the interdomain separation in DnaK, the major bacterial heat shock protein 70 (Hsp70). The interdomain distance increases from 47 Å in the ATP-bound state to 84 Å in the ADP-bound state and slightly contracts to 77 Å when a substrate is bound. This is in contrast to what was observed for the mitochondrial member of the Hsp70s, Ssc1, supporting the notion of evolutionary specialization of Hsp70s for different cellular functions in different organisms and cell organelles.
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Affiliation(s)
- Volodymyr Kudryavtsev
- Physical Chemistry, Department of Chemistry, Munich Center for Integrated Protein Science (CiPSM) and Center for Nanoscience, Ludwig-Maximilians-Universität München, Butenandtstr. 11, Gerhard-Ertl-Building, 81377 Munich, Germany
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39
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Cristóvão M, Sisamakis E, Hingorani MM, Marx AD, Jung CP, Rothwell PJ, Seidel CAM, Friedhoff P. Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA. Nucleic Acids Res 2012; 40:5448-64. [PMID: 22367846 PMCID: PMC3384296 DOI: 10.1093/nar/gks138] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mismatch repair (MMR) corrects replication errors such as mismatched bases and loops in DNA. The evolutionarily conserved dimeric MMR protein MutS recognizes mismatches by stacking a phenylalanine of one subunit against one base of the mismatched pair. In all crystal structures of G:T mismatch-bound MutS, phenylalanine is stacked against thymine. To explore whether these structures reflect directional mismatch recognition by MutS, we monitored the orientation of Escherichia coli MutS binding to mismatches by FRET and anisotropy with steady state, pre-steady state and single-molecule multiparameter fluorescence measurements in a solution. The results confirm that specifically bound MutS bends DNA at the mismatch. We found additional MutS–mismatch complexes with distinct conformations that may have functional relevance in MMR. The analysis of individual binding events reveal significant bias in MutS orientation on asymmetric mismatches (G:T versus T:G, A:C versus C:A), but not on symmetric mismatches (G:G). When MutS is blocked from binding a mismatch in the preferred orientation by positioning asymmetric mismatches near the ends of linear DNA substrates, its ability to authorize subsequent steps of MMR, such as MutH endonuclease activation, is almost abolished. These findings shed light on prerequisites for MutS interactions with other MMR proteins for repairing the appropriate DNA strand.
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Affiliation(s)
- Michele Cristóvão
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Evangelos Sisamakis
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Manju M. Hingorani
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Andreas D. Marx
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Caroline P. Jung
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Paul J. Rothwell
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
| | - Claus A. M. Seidel
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
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40
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Schuler B, Müller-Späth S, Soranno A, Nettels D. Application of confocal single-molecule FRET to intrinsically disordered proteins. Methods Mol Biol 2012; 896:21-45. [PMID: 22821515 DOI: 10.1007/978-1-4614-3704-8_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a large degree of conformational heterogeneity. In such cases, classical experimental methods often yield only mean values, averaged over the entire ensemble of molecules. The microscopic distributions of conformations, trajectories, or sequences of events often remain unknown, and with them the underlying molecular mechanisms. Signal averaging can be avoided by observing individual molecules. A particularly versatile method is highly sensitive fluorescence detection. In combination with Förster resonance energy transfer (FRET), distances and conformational dynamics can be investigated in single molecules. This chapter introduces the practical aspects of applying confocal single-molecule FRET experiments to the study of IDPs.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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41
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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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Hoefling M, Lima N, Haenni D, Seidel CAM, Schuler B, Grubmüller H. Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. PLoS One 2011; 6:e19791. [PMID: 21629703 PMCID: PMC3101224 DOI: 10.1371/journal.pone.0019791] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 04/05/2011] [Indexed: 11/21/2022] Open
Abstract
Förster Resonance Energy Transfer (FRET) experiments probe molecular distances via distance dependent energy transfer from an excited donor dye to an acceptor dye. Single molecule experiments not only probe average distances, but also distance distributions or even fluctuations, and thus provide a powerful tool to study biomolecular structure and dynamics. However, the measured energy transfer efficiency depends not only on the distance between the dyes, but also on their mutual orientation, which is typically inaccessible to experiments. Thus, assumptions on the orientation distributions and averages are usually made, limiting the accuracy of the distance distributions extracted from FRET experiments. Here, we demonstrate that by combining single molecule FRET experiments with the mutual dye orientation statistics obtained from Molecular Dynamics (MD) simulations, improved estimates of distances and distributions are obtained. From the simulated time-dependent mutual orientations, FRET efficiencies are calculated and the full statistics of individual photon absorption, energy transfer, and photon emission events is obtained from subsequent Monte Carlo (MC) simulations of the FRET kinetics. All recorded emission events are collected to bursts from which efficiency distributions are calculated in close resemblance to the actual FRET experiment, taking shot noise fully into account. Using polyproline chains with attached Alexa 488 and Alexa 594 dyes as a test system, we demonstrate the feasibility of this approach by direct comparison to experimental data. We identified cis-isomers and different static local environments as sources of the experimentally observed heterogeneity. Reconstructions of distance distributions from experimental data at different levels of theory demonstrate how the respective underlying assumptions and approximations affect the obtained accuracy. Our results show that dye fluctuations obtained from MD simulations, combined with MC single photon kinetics, provide a versatile tool to improve the accuracy of distance distributions that can be extracted from measured single molecule FRET efficiencies.
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Affiliation(s)
- Martin Hoefling
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Nicola Lima
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dominik Haenni
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Claus A. M. Seidel
- Institute of Molecular Physical Chemistry (MPC), Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Sindbert S, Kalinin S, Nguyen H, Kienzler A, Clima L, Bannwarth W, Appel B, Müller S, Seidel CAM. Accurate Distance Determination of Nucleic Acids via Förster Resonance Energy Transfer: Implications of Dye Linker Length and Rigidity. J Am Chem Soc 2011; 133:2463-80. [DOI: 10.1021/ja105725e] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon Sindbert
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany
| | - Hien Nguyen
- Institut für Biochemie, Bioorganische Chemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Andrea Kienzler
- Fakultät für Chemie und Biochemie, Albert-Ludwigs Universität Freiburg, AK Bannwarth, Albertstrasse 21, 79104, Freiburg, Germany
| | - Lilia Clima
- Fakultät für Chemie und Biochemie, Albert-Ludwigs Universität Freiburg, AK Bannwarth, Albertstrasse 21, 79104, Freiburg, Germany
| | - Willi Bannwarth
- Fakultät für Chemie und Biochemie, Albert-Ludwigs Universität Freiburg, AK Bannwarth, Albertstrasse 21, 79104, Freiburg, Germany
| | - Bettina Appel
- Institut für Biochemie, Bioorganische Chemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Bioorganische Chemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany
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Abstract
Molecular diffusion and transport processes are fundamental in physical, chemical, and biological systems. Current approaches to measuring molecular transport in cells and tissues based on perturbation methods, e.g., fluorescence recovery after photobleaching, are invasive; single-point fluctuation correlation methods are local; and single-particle tracking requires the observation of isolated particles for relatively long periods of time. We discuss here the detection of molecular transport by exploiting spatiotemporal correlations measured among points at large distances (>1 μm). We illustrate the evolution of the conceptual framework that started with single-point fluorescence fluctuation analysis based on the transit of fluorescent molecules through a small volume of illumination. This idea has evolved to include the measurement of fluctuations at many locations in the sample using microscopy imaging methods. Image fluctuation analysis has become a rich and powerful technique that can be used to extract information about the spatial distribution of molecular concentration and transport in cells and tissues.
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Affiliation(s)
- Michelle A Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA
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Kalinin S, Valeri A, Antonik M, Felekyan S, Seidel CAM. Detection of structural dynamics by FRET: a photon distribution and fluorescence lifetime analysis of systems with multiple states. J Phys Chem B 2010; 114:7983-95. [PMID: 20486698 DOI: 10.1021/jp102156t] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two complementary methods in confocal single-molecule fluorescence spectroscopy are presented to analyze conformational dynamics by Forster resonance energy transfer (FRET) measurements considering simulated and experimental data. First, an extension of photon distribution analysis (PDA) is applied to characterize conformational exchange between two or more states via global analysis of the shape of FRET peaks for different time bins. PDA accurately predicts the shape of FRET efficiency histograms in the presence of FRET fluctuations, taking into account shot noise and background contributions. Dynamic-PDA quantitatively recovers FRET efficiencies of the interconverting states and relaxation times of dynamics on the time scale of the diffusion time t(d) (typically milliseconds), with a dynamic range of the method of about +/-1 order of magnitude with respect to t(d). Correction procedures are proposed to consider the factors limiting the accuracy of dynamic-PDA, such as brightness variations, shortening of the observation time due to diffusion, and a contribution of multimolecular events. Second, an analysis procedure for multiparameter fluorescence detection is presented, where intensity-derived FRET efficiency is correlated with the fluorescence lifetime of the donor quenched by FRET. If a maximum likelihood estimator is applied to compute a mean fluorescence lifetime of mixed states, one obtains a fluorescence weighted mean lifetime. Thus a mixed state is detected by a characteristic shift of the fluorescence lifetime, which becomes longer than that expected for a single species with the same intensity-derived FRET efficiency. Analysis tools for direct visual inspection of two-dimensional diagrams of FRET efficiency versus donor lifetime are presented for the cases of static and dynamic FRET. Finally these new techniques are compared with fluorescence correlation spectroscopy.
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Affiliation(s)
- Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany.
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Hohlbein J, Gryte K, Heilemann M, Kapanidis AN. Surfing on a new wave of single-molecule fluorescence methods. Phys Biol 2010; 7:031001. [DOI: 10.1088/1478-3975/7/3/031001] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Santoso Y, Torella JP, Kapanidis AN. Characterizing Single-Molecule FRET Dynamics with Probability Distribution Analysis. Chemphyschem 2010; 11:2209-19. [DOI: 10.1002/cphc.201000129] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mapa K, Sikor M, Kudryavtsev V, Waegemann K, Kalinin S, Seidel CAM, Neupert W, Lamb DC, Mokranjac D. The conformational dynamics of the mitochondrial Hsp70 chaperone. Mol Cell 2010; 38:89-100. [PMID: 20385092 DOI: 10.1016/j.molcel.2010.03.010] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2009] [Revised: 02/03/2010] [Accepted: 03/22/2010] [Indexed: 12/31/2022]
Abstract
Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular chaperones involved in a plethora of cellular processes. The dynamics of their ATP hydrolysis-driven and cochaperone-regulated conformational cycle are poorly understood. We used fluorescence spectroscopy to analyze, in real time and at single-molecule resolution, the effects of nucleotides and cochaperones on the conformation of Ssc1, a mitochondrial member of the family. We report that the conformation of its ADP state is unexpectedly heterogeneous, in contrast to a uniform ATP state. Substrates are actively involved in determining the conformation of Ssc1. The J protein Mdj1 does not interact transiently with the chaperone, as generally believed, but rather is released slowly upon ATP hydrolysis. Analysis of the major bacterial Hsp70 revealed important differences between highly homologous members of the family, possibly explaining tuning of Hsp70 chaperones to meet specific functions in different organisms and cellular compartments.
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Affiliation(s)
- Koyeli Mapa
- Institute for Physiological Chemistry, LMU München, 81377 Munich, Germany
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Kalinin S, Sisamakis E, Magennis SW, Felekyan S, Seidel CAM. On the Origin of Broadening of Single-Molecule FRET Efficiency Distributions beyond Shot Noise Limits. J Phys Chem B 2010; 114:6197-206. [DOI: 10.1021/jp100025v] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Evangelos Sisamakis
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Steven W. Magennis
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
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