51
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Krüger TPJ, Ilioaia C, Johnson MP, Belgio E, Horton P, Ruban AV, van Grondelle R. The specificity of controlled protein disorder in the photoprotection of plants. Biophys J 2014; 105:1018-26. [PMID: 23972853 DOI: 10.1016/j.bpj.2013.07.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/11/2013] [Accepted: 07/15/2013] [Indexed: 11/28/2022] Open
Abstract
Light-harvesting pigment-protein complexes of photosystem II of plants have a dual function: they efficiently use absorbed energy for photosynthesis at limiting sunlight intensity and dissipate the excess energy at saturating intensity for photoprotection. Recent single-molecule spectroscopy studies on the trimeric LHCII complex showed that environmental control of the intrinsic protein disorder could in principle explain the switch between their light-harvesting and photoprotective conformations in vivo. However, the validity of this proposal depends strongly on the specificity of the protein dynamics. Here, a similar study has been performed on the minor monomeric antenna complexes of photosystem II (CP29, CP26, and CP24). Despite their high structural homology, similar pigment content and organization compared to LHCII trimers, the environmental response of these proteins was found to be rather distinct. A much larger proportion of the minor antenna complexes were present in permanently weakly fluorescent states under most conditions used; however, unlike LHCII trimers the distribution of the single-molecule population between the strongly and weakly fluorescent states showed no significant sensitivity to low pH, zeaxanthin, or low detergent conditions. The results support a unique role for LHCII trimers in the regulation of light harvesting by controlled fluorescence blinking and suggest that any contribution of the minor antenna complexes to photoprotection would probably involve a distinct mechanism.
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Affiliation(s)
- Tjaart P J Krüger
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands.
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52
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Bockenhauer SD, Duncan TM, Moerner WE, Börsch M. The regulatory switch of F 1-ATPase studied by single-molecule FRET in the ABEL Trap. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8950:89500H. [PMID: 25309100 DOI: 10.1117/12.2042688] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
F1-ATPase is the soluble portion of the membrane-embedded enzyme FoF1-ATP synthase that catalyzes the production of adenosine triphosphate in eukaryotic and eubacterial cells. In reverse, the F1 part can also hydrolyze ATP quickly at three catalytic binding sites. Therefore, catalysis of 'non-productive' ATP hydrolysis by F1 (or FoF1) must be minimized in the cell. In bacteria, the ε subunit is thought to control and block ATP hydrolysis by mechanically inserting its C-terminus into the rotary motor region of F1. We investigate this proposed mechanism by labeling F1 specifically with two fluorophores to monitor the C-terminus of the ε subunit by Förster resonance energy transfer. Single F1 molecules are trapped in solution by an Anti-Brownian electrokinetic trap which keeps the FRET-labeled F1 in place for extended observation times of several hundreds of milliseconds, limited by photobleaching. FRET changes in single F1 and FRET histograms for different biochemical conditions are compared to evaluate the proposed regulatory mechanism.
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Affiliation(s)
- Samuel D Bockenhauer
- Department of Chemistry, Stanford University, Stanford, CA, USA ; Department of Physics, Stanford University, Stanford, CA, USA
| | - Thomas M Duncan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany
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53
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Single-molecule motions enable direct visualization of biomolecular interactions in solution. Nat Methods 2014; 11:555-8. [PMID: 24608179 DOI: 10.1038/nmeth.2882] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 01/25/2014] [Indexed: 11/08/2022]
Abstract
Biomolecular interactions are generally accompanied by modifications in size and charge of biomolecules at the nanometer scale. Here we describe a single-molecule method to sense these changes in real time based on statistical learning of diffusive and electric field-induced motion parameters of a trapped molecule in solution. We demonstrate the approach by resolving a monomer-trimer mixture along a protein dissociation pathway and visualizing the binding-unbinding kinetics of a single DNA molecule.
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54
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Maksimov EG, Schmitt FJ, Shirshin EA, Svirin MD, Elanskaya IV, Friedrich T, Fadeev VV, Paschenko VZ, Rubin AB. The time course of non-photochemical quenching in phycobilisomes of Synechocystis sp. PCC6803 as revealed by picosecond time-resolved fluorimetry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1540-7. [PMID: 24463052 DOI: 10.1016/j.bbabio.2014.01.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/25/2013] [Accepted: 01/15/2014] [Indexed: 11/29/2022]
Abstract
As high-intensity solar radiation can lead to extensive damage of the photosynthetic apparatus, cyanobacteria have developed various protection mechanisms to reduce the effective excitation energy transfer (EET) from the antenna complexes to the reaction center. One of them is non-photochemical quenching (NPQ) of the phycobilisome (PB) fluorescence. In Synechocystis sp. PCC6803 this role is carried by the orange carotenoid protein (OCP), which reacts to high-intensity light by a series of conformational changes, enabling the binding of OCP to the PBs reducing the flow of energy into the photosystems. In this paper the mechanisms of energy migration in two mutant PB complexes of Synechocystis sp. were investigated and compared. The mutant CK is lacking phycocyanin in the PBs while the mutant ΔPSI/PSII does not contain both photosystems. Fluorescence decay spectra with picosecond time resolution were registered using a single photon counting technique. The studies were performed in a wide range of temperatures - from 4 to 300 K. The time course of NPQ and fluorescence recovery in darkness was studied at room temperature using both steady-state and time-resolved fluorescence measurements. The OCP induced NPQ has been shown to be due to EET from PB cores to the red form of OCP under photon flux densities up to 1000 μmolphotonsm⁻²s⁻¹. The gradual changes of the energy transfer rate from allophycocyanin to OCP were observed during the irradiation of the sample with blue light and consequent adaptation to darkness. This fact was interpreted as the revelation of intermolecular interaction between OCP and PB binding site. At low temperatures a significantly enhanced EET from allophycocyanin to terminal emitters has been shown, due to the decreased back transfer from terminal emitter to APC. The activation of OCP not only leads to fluorescence quenching, but also affects the rate constants of energy transfer as shown by model based analysis of the decay associated spectra. The results indicate that the ability of OCP to quench the fluorescence is strongly temperature dependent. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy.
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Affiliation(s)
- E G Maksimov
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia.
| | - F-J Schmitt
- Institute of Chemistry, Biophysical Chemistry, TU Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - E A Shirshin
- Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - M D Svirin
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - I V Elanskaya
- Department of Genetics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - T Friedrich
- Institute of Chemistry, Biophysical Chemistry, TU Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - V V Fadeev
- Department of Quantum Electronics, Faculty of Physics, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - V Z Paschenko
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - A B Rubin
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
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55
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JØRGENSEN SUNEK, HATZAKIS NIKOSS. INSIGHTS IN ENZYME FUNCTIONAL DYNAMICS AND ACTIVITY REGULATION BY SINGLE MOLECULE STUDIES. ACTA ACUST UNITED AC 2014. [DOI: 10.1142/s1793048013300028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The advent of advanced single molecule measurements heralded the arrival of a wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways not deducible by conventional bulk assays. They offered the direct observation and quantification of the abundance and life time of multiple states and transient intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements, thus providing unprecedented insights into complex biological processes. Here we survey the current state of the art in single-molecule fluorescence microscopy methodology for studying the mechanism of enzymatic activity and the insights on protein functional dynamics. We will initially discuss the strategies employed to date, their limitations and possible ways to overcome them, and finally how single enzyme kinetics can advance our understanding on mechanisms underlying function and regulation of proteins. [Formula: see text]Special Issue Comment: This review focuses on functional dynamics of individual enzymes and is related to the review on ion channels by Lu,44 the reviews on mathematical treatment of Flomenbom45 and Sach et al.,46 and review on FRET by Ruedas-Rama et al.41
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Affiliation(s)
- SUNE K. JØRGENSEN
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
| | - NIKOS S. HATZAKIS
- Bio-Nanotechnology Laboratory, Department of Chemistry, Nano-Science Center, Lundbeck Foundation Center, Biomembranes in Nanomedicine University of Copenhagen, 2100 Copenhagen, Denmark
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56
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Schlau-Cohen GS, Bockenhauer S, Wang Q, Moerner WE. Single-molecule spectroscopy of photosynthetic proteins in solution: exploration of structure–function relationships. Chem Sci 2014. [DOI: 10.1039/c4sc00582a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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57
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Dendrimer probes for enhanced photostability and localization in fluorescence imaging. Biophys J 2013; 104:1566-75. [PMID: 23561533 DOI: 10.1016/j.bpj.2013.01.052] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 01/21/2013] [Accepted: 01/28/2013] [Indexed: 01/08/2023] Open
Abstract
Recent advances in fluorescence microscopy have enabled high-resolution imaging and tracking of single proteins and biomolecules in cells. To achieve high spatial resolutions in the nanometer range, bright and photostable fluorescent probes are critically required. From this view, there is a strong need for development of advanced fluorescent probes with molecular-scale dimensions for fluorescence imaging. Polymer-based dendrimer nanoconjugates hold strong potential to serve as versatile fluorescent probes due to an intrinsic capacity for tailored spectral properties such as brightness and emission wavelength. In this work, we report a new, to our knowledge, class of molecular probes based on dye-conjugated dendrimers for fluorescence imaging and single-molecule fluorescence microscopy. We engineered fluorescent dendritic nanoprobes (FDNs) to contain multiple organic dyes and reactive groups for target-specific biomolecule labeling. The photophysical properties of dye-conjugated FDNs (Cy5-FDNs and Cy3-FDNs) were characterized using single-molecule fluorescence microscopy, which revealed greatly enhanced photostability, increased probe brightness, and improved localization precision in high-resolution fluorescence imaging compared to single organic dyes. As proof-of-principle demonstration, Cy5-FDNs were used to assay single-molecule nucleic acid hybridization and for immunofluorescence imaging of microtubules in cytoskeletal networks. In addition, Cy5-FDNs were used as reporter probes in a single-molecule protein pull-down assay to characterize antibody binding and target protein capture. In all cases, the photophysical properties of FDNs resulted in enhanced fluorescence imaging via improved brightness and/or photostability.
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58
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Bockenhauer SD, Moerner WE. Photo-induced conformational flexibility in single solution-phase peridinin-chlorophyll-proteins. J Phys Chem A 2013; 117:8399-406. [PMID: 23919352 DOI: 10.1021/jp405790a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The peridinin-chlorophyll-protein (PCP) is an accessory light-harvesting complex found in red-tide dinoflagellates. PCP absorbs photons primarily in the blue-green spectral region via peridinin (Per) carotenoid pigments which then transfer excitations to chlorophyll (Chl) and ultimately downstream to photosystem II (PSII). Whereas the ultrafast dynamics of PCP are well-studied, much less is known about slower protein dynamics on time scales of milliseconds and seconds. Previous single-molecule studies of spectral emission and intensity have attached PCP to surfaces, but the native environment of PCP is in the lumen, meaning that a surface-attached environment could perturb its native conformations. To address this concern, we use the anti-Brownian electrokinetic (ABEL) trap to study single PCP monomers in solution for several seconds each. We measure, for the first time, simultaneous single-molecule intensity, lifetime, and spectral emission shifts for each trapped PCP monomer. The rate of reversible spectral redshifts depends linearly on irradiance over a factor of 30, indicating a light-induced mechanism which we attribute to a protein conformational change. Independent of these spectral shifts, our measurements of intensity and lifetime show reversible Chl quenching. In contrast to previous work, we show that this quenching cannot result from isolated photobleaching of Chl. These independent mechanisms arise from distinct conformational changes which maintain relatively stable fluorescence emission.
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59
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Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states. Proc Natl Acad Sci U S A 2013; 110:10899-903. [PMID: 23776245 DOI: 10.1073/pnas.1310222110] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Photosynthetic organisms flourish under low light intensities by converting photoenergy to chemical energy with near unity quantum efficiency and under high light intensities by safely dissipating excess photoenergy and deleterious photoproducts. The molecular mechanisms balancing these two functions remain incompletely described. One critical barrier to characterizing the mechanisms responsible for these processes is that they occur within proteins whose excited-state properties vary drastically among individual proteins and even within a single protein over time. In ensemble measurements, these excited-state properties appear only as the average value. To overcome this averaging, we investigate the purple bacterial antenna protein light harvesting complex 2 (LH2) from Rhodopseudomonas acidophila at the single-protein level. We use a room-temperature, single-molecule technique, the anti-Brownian electrokinetic trap, to study LH2 in a solution-phase (nonperturbative) environment. By performing simultaneous measurements of fluorescence intensity, lifetime, and spectra of single LH2 complexes, we identify three distinct states and observe transitions occurring among them on a timescale of seconds. Our results reveal that LH2 complexes undergo photoactivated switching to a quenched state, likely by a conformational change, and thermally revert to the ground state. This is a previously unobserved, reversible quenching pathway, and is one mechanism through which photosynthetic organisms can adapt to changes in light intensities.
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60
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Börsch M. Microscopy of single F(o) F(1) -ATP synthases--the unraveling of motors, gears, and controls. IUBMB Life 2013; 65:227-37. [PMID: 23378185 DOI: 10.1002/iub.1149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/12/2013] [Indexed: 11/09/2022]
Abstract
Optical microscopy of single F(1) -ATPase and F(o) F(1) -ATP synthases started 15 years ago. Direct demonstration of ATP-driven subunit rotation by videomicroscopy became the new exciting tool to analyze the conformational changes of this enzyme during catalysis. Stimulated by these experiments, technical improvements for higher time resolution, better angular resolution, and reduced viscous drag were developed rapidly. Optics and single-molecule enzymology were entangled to benefit both biochemists and microscopists. Today, several single-molecule microscopy methods are established including controls for the precise nanomanipulation of individual enzymes in vitro. Förster resonance energy transfer, which has been used for simultaneous monitoring of conformational changes of different parts of this rotary motor, is one of them and may become the tool for the analysis of single F(o) F(1) -ATP synthases in membranes of living cells. Here, breakthrough experiments are critically reviewed and challenges are discussed for the future microscopy of single ATP synthesizing enzymes at work.
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Affiliation(s)
- Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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61
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Yin Y, Yuan R, Zhao XS. Amplitude of Relaxations in Fluorescence Correlation Spectroscopy for Fluorophores That Diffuse Together. J Phys Chem Lett 2013; 4:304-309. [PMID: 26283439 DOI: 10.1021/jz301871f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The amplitude of chemical relaxations in fluorescence correlation spectroscopy (FCS) is an important parameter that directly relates to not only the equilibrium constant of the relaxations but also the number of individual fluorophores that diffuse together. In this Letter we answer the question how exactly the amplitude of the relaxations in FCS changes with respect to the number of identical fluorophores on one cargo. We anchored tetramethylrhodamine molecules onto each arm of a DNA Holliday junction molecule so that the codiffusing dyes were capable of performing independent fluorescent fluctuations. We found that the amplitudes of the relaxations were inversely proportional to the number of the dyes on each cargo molecule, well agreeing with the theoretical prediction derived in this Letter. The result provides a guideline for the FCS data analysis and points out a simple way to determine the number of molecules that a cargo carries.
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Affiliation(s)
- Yandong Yin
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Rongfeng Yuan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Xin Sheng Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, 100871, China
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62
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Sielaff H, Börsch M. Twisting and subunit rotation in single F(O)(F1)-ATP synthase. Philos Trans R Soc Lond B Biol Sci 2012; 368:20120024. [PMID: 23267178 DOI: 10.1098/rstb.2012.0024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
F(O)F(1)-ATP synthases are ubiquitous proton- or ion-powered membrane enzymes providing ATP for all kinds of cellular processes. The mechanochemistry of catalysis is driven by two rotary nanomotors coupled within the enzyme. Their different step sizes have been observed by single-molecule microscopy including videomicroscopy of fluctuating nanobeads attached to single enzymes and single-molecule Förster resonance energy transfer. Here we review recent developments of approaches to monitor the step size of subunit rotation and the transient elastic energy storage mechanism in single F(O)F(1)-ATP synthases.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Nonnenplan 2-4, 07743 Jena, Germany
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63
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Wang Q, Moerner WE. Lifetime and Spectrally Resolved Characterization of the Photodynamics of Single Fluorophores in Solution Using the Anti-Brownian Electrokinetic Trap. J Phys Chem B 2012. [DOI: 10.1021/jp308949d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quan Wang
- Department
of Chemistry and ‡Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry and ‡Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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64
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Wang Q, Goldsmith RH, Jiang Y, Bockenhauer SD, Moerner W. Probing single biomolecules in solution using the anti-Brownian electrokinetic (ABEL) trap. Acc Chem Res 2012; 45:1955-64. [PMID: 22616716 DOI: 10.1021/ar200304t] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single-molecule fluorescence measurements allow researchers to study asynchronous dynamics and expose molecule-to-molecule structural and behavioral diversity, which contributes to the understanding of biological macromolecules. To provide measurements that are most consistent with the native environment of biomolecules, researchers would like to conduct these measurements in the solution phase if possible. However, diffusion typically limits the observation time to approximately 1 ms in many solution-phase single-molecule assays. Although surface immobilization is widely used to address this problem, this process can perturb the system being studied and contribute to the observed heterogeneity. Combining the technical capabilities of high-sensitivity single-molecule fluorescence microscopy, real-time feedback control and electrokinetic flow in a microfluidic chamber, we have developed a device called the anti-Brownian electrokinetic (ABEL) trap to significantly prolong the observation time of single biomolecules in solution. We have applied the ABEL trap method to explore the photodynamics and enzymatic properties of a variety of biomolecules in aqueous solution and present four examples: the photosynthetic antenna allophycocyanin, the chaperonin enzyme TRiC, a G protein-coupled receptor protein, and the blue nitrite reductase redox enzyme. These examples illustrate the breadth and depth of information which we can extract in studies of single biomolecules with the ABEL trap. When confined in the ABEL trap, the photosynthetic antenna protein allophycocyanin exhibits rich dynamics both in its emission brightness and its excited state lifetime. As each molecule discontinuously converts from one emission/lifetime level to another in a primarily correlated way, it undergoes a series of state changes. We studied the ATP binding stoichiometry of the multi-subunit chaperonin enzyme TRiC in the ABEL trap by counting the number of hydrolyzed Cy3-ATP using stepwise photobleaching. Unlike ensemble measurements, the observed ATP number distributions depart from the standard cooperativity models. Single copies of detergent-stabilized G protein-coupled receptor proteins labeled with a reporter fluorophore also show discontinuous changes in emission brightness and lifetime, but the various states visited by the single molecules are broadly distributed. As an agonist binds, the distributions shift slightly toward a more rigid conformation of the protein. By recording the emission of a reporter fluorophore which is quenched by reduction of a nearby type I Cu center, we probed the enzymatic cycle of the redox enzyme nitrate reductase. We determined the rate constants of a model of the underlying kinetics through an analysis of the dwell times of the high/low intensity levels of the fluorophore versus nitrite concentration.
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Affiliation(s)
- Quan Wang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Randall H. Goldsmith
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Yan Jiang
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - Samuel D. Bockenhauer
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
| | - W.E. Moerner
- Department of Chemistry, ‡Department of Electrical Engineering, §Department of Applied Physics, ∥Department of Physics, Stanford University, Stanford, California, United States
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65
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Hughes AJ, Tentori AM, Herr AE. Bistable isoelectric point photoswitching in green fluorescent proteins observed by dynamic immunoprobed isoelectric focusing. J Am Chem Soc 2012; 134:17582-91. [PMID: 23017083 PMCID: PMC3488114 DOI: 10.1021/ja3064292] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We describe a novel isoelectric point photoswitching phenomenon in both wild-type Aequorea victoria (av) GFP and the amino acid 222 E-to-G mutant Aequorea coerulescens (ac) GFP. A combination of time-resolved microfluidic isoelectric focusing (IEF) and in situ antibody blotting IEF was employed to monitor dark (nonfluorescent) and bright (fluorescent) GFP populations. Through IEF, each population was observed to exhibit distinct isoelectric points (pI) and, thus, distinct formal electrostatic charges. Experimentally observed interconversion between the dark, higher pI and bright, lower pI GFP populations is tightly controlled by differential UV and blue light exposure. The stoichiometry and kinetics of charge transfer tied to this reversible photobleaching process are deduced. In concert with a reaction-transport model of bistable reversible charge and fluorescence photoswitching, the on-chip measurements of population interconversion rates suggest the potential for both rheostatic and discrete switch-like modulation of the electrostatic charge of GFPs depending on the illumination profile. We estimate that 3-4 formal charges distinguish the bright and dark populations of avGFP, as compared to one charge for those of acGFP. Given the proposed role of E222 as a bridge between internal and exit hydrogen-bond clusters within the GFP β-barrel, the difference in charge switching magnitude between the two mutants provides intriguing evidence for the proton wire hypothesis of proton transport within the GFP structure, and of proton exchange with the bulk solvent. Our facile dynamic and probed IEF assays should find widespread use in analytical screening and quantitative kinetic analysis of photoswitching and other charge switching processes in response to stimuli including light, temperature, or binding/cleavage events.
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Affiliation(s)
- Alex J Hughes
- Department of Bioengineering and the UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720, USA
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66
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Ernst S, Düser MG, Zarrabi N, Dunn SD, Börsch M. Elastic deformations of the rotary double motor of single FoF1-ATP synthases detected in real time by Förster resonance energy transfer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1722-31. [DOI: 10.1016/j.bbabio.2012.03.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/25/2012] [Accepted: 03/29/2012] [Indexed: 11/17/2022]
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67
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Abstract
Optical tracking of a fluorescent particle in solution faces fundamental constraints due to Brownian motion, diffraction, and photon shot noise. Background photons and imperfect tracking apparatus further degrade tracking precision. Here we use a model of particle motion to combine information from multiple time-points to improve the localization precision. We derive successive approximations that enable real-time particle tracking with well controlled tradeoffs between precision and computational cost. We present the theory in the context of feedback electrokinetic trapping, though the results apply to optical tracking of any particle subject to diffusion and drift. We use numerical simulations and experimental data to validate the algorithms' performance.
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Affiliation(s)
- Alexander P Fields
- Center for Ultrasound Molecular Imaging and Therapeutics, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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68
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Affiliation(s)
- Min Ju Shon
- Department of Chemistry
and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138,
United States
| | - Adam E. Cohen
- Department of Chemistry
and Chemical Biology and Department of Physics, Harvard University, Cambridge, Massachusetts 02138,
United States
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69
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Dawlaty JM, Ishizaki A, De AK, Fleming GR. Microscopic quantum coherence in a photosynthetic-light-harvesting antenna. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:3672-91. [PMID: 22753820 DOI: 10.1098/rsta.2011.0207] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We briefly review the coherent quantum beats observed in recent two-dimensional electronic spectroscopy experiments in a photosynthetic-light-harvesting antenna. We emphasize that the decay of the quantum beats in these experiments is limited by ensemble averaging. The in vivo dynamics of energy transport depends upon the local fluctuations of a single photosynthetic complex during the energy transfer time (a few picoseconds). Recent analyses suggest that it remains possible that the quantum-coherent motion may be robust under individual realizations of the environment-induced fluctuations contrary to intuition obtained from condensed phase spectroscopic measurements and reduced density matrices. This result indicates that the decay of the observed quantum coherence can be understood as ensemble dephasing. We propose a fluorescence-detected single-molecule experiment with phase-locked excitation pulses to investigate the coherent dynamics at the level of a single molecule without hindrance by ensemble averaging. We discuss the advantages and limitations of this method. We report our initial results on bulk fluorescence-detected coherent spectroscopy of the Fenna-Mathews-Olson complex.
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Affiliation(s)
- Jahan M Dawlaty
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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Kamagata K, Kawaguchi T, Iwahashi Y, Baba A, Fujimoto K, Komatsuzaki T, Sambongi Y, Goto Y, Takahashi S. Long-Term Observation of Fluorescence of Free Single Molecules To Explore Protein-Folding Energy Landscapes. J Am Chem Soc 2012; 134:11525-32. [DOI: 10.1021/ja3020555] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Kiyoto Kamagata
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai
980-8577, Japan
| | - Toshifumi Kawaguchi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai
980-8577, Japan
| | - Yoshitomo Iwahashi
- Optonica Corporation, 1-26-11, Matsuigaoka, Kyotanabe,
Kyoto 610-0353, Japan
| | - Akinori Baba
- RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi,
Chuo-ku, Kobe 650-0047, Japan
| | - Kazuya Fujimoto
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tamiki Komatsuzaki
- Molecule & Life Nonlinear Sciences Laboratory, Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
- Core Research for Evolutional Science and
Technology, Japan Science and Technology Agency, 4-1-8, Honmachi, Kawaguchi, Saitama 332-0012, Japan
| | - Yoshihiro Sambongi
- Core Research for Evolutional Science and
Technology, Japan Science and Technology Agency, 4-1-8, Honmachi, Kawaguchi, Saitama 332-0012, Japan
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4, Kagamiyama, Higashi-Hiroshima,
Hiroshima 739-8528, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Takahashi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai
980-8577, Japan
- Core Research for Evolutional Science and
Technology, Japan Science and Technology Agency, 4-1-8, Honmachi, Kawaguchi, Saitama 332-0012, Japan
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71
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Lesoine JF, Venkataraman PA, Maloney PC, Dumont M, Novotny L. Nanochannel-based single molecule recycling. NANO LETTERS 2012; 12:3273-8. [PMID: 22662745 PMCID: PMC3377747 DOI: 10.1021/nl301341m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We present a method for measuring the fluorescence from a single molecule hundreds of times without surface immobilization. The approach is based on the use of electroosmosis to repeatedly drive a single target molecule in a fused silica nanochannel through a stationary laser focus. Single molecule fluorescence detected during the transit time through the laser focus is used to repeatedly reverse the electrical potential controlling the flow direction. Our method does not rely on continuous observation and therefore is less susceptible to fluorescence blinking than existing fluorescence-based trapping schemes. The variation in the turnaround times can be used to measure the diffusion coefficient on a single molecule level. We demonstrate the ability to recycle both proteins and DNA in nanochannels and show that the procedure can be combined with single-pair Förster energy transfer. Nanochannel-based single molecule recycling holds promise for studying conformational dynamics on the same single molecule in solution and without surface tethering.
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Affiliation(s)
- John F. Lesoine
- Institute of Optics, University of Rochester, Rochester NY 14627
| | - Prahnesh A. Venkataraman
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627
| | - Peter C. Maloney
- Department of Physiology, Johns Hopkins Medical School, Baltimore, MD, USA
| | - Mark Dumont
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627
| | - Lukas Novotny
- Institute of Optics, University of Rochester, Rochester NY 14627
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72
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Sandén T, Wyss R, Santschi C, Hassaïne G, Deluz C, Martin OJF, Wennmalm S, Vogel H. A zeptoliter volume meter for analysis of single protein molecules. NANO LETTERS 2012; 12:370-375. [PMID: 22149182 DOI: 10.1021/nl2036468] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A central goal in bioanalytics is to determine the concentration of and interactions between biomolecules. Nanotechnology allows performing such analyses in a highly parallel, low-cost, and miniaturized fashion. Here we report on label-free volume, concentration, and mobility analysis of single protein molecules and nanoparticles during their diffusion through a subattoliter detection volume, confined by a 100 nm aperture in a thin gold film. A high concentration of small fluorescent molecules renders the aqueous solution in the aperture brightly fluorescent. Nonfluorescent analytes diffusing into the aperture displace the fluorescent molecules in the solution, leading to a decrease of the detected fluorescence signal, while analytes diffusing out of the aperture return the fluorescence level. The resulting fluorescence fluctuations provide direct information on the volume, concentration, and mobility of the nonfluorescent analytes through fluctuation analysis in both time and amplitude.
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Affiliation(s)
- Tor Sandén
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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73
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Lee HC, Lin BL, Chang WH, Tu IP. Toward automated denoising of single molecular Förster resonance energy transfer data. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:011007. [PMID: 22352641 DOI: 10.1117/1.jbo.17.1.011007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A wide-field two-channel fluorescence microscope is a powerful tool as it allows for the study of conformation dynamics of hundreds to thousands of immobilized single molecules by Förster resonance energy transfer (FRET) signals. To date, the data reduction from a movie to a final set containing meaningful single-molecule FRET (smFRET) traces involves human inspection and intervention at several critical steps, greatly hampering the efficiency at the post-imaging stage. To facilitate the data reduction from smFRET movies to smFRET traces and to address the noise-limited issues, we developed a statistical denoising system toward fully automated processing. This data reduction system has embedded several novel approaches. First, as to background subtraction, high-order singular value decomposition (HOSVD) method is employed to extract spatial and temporal features. Second, to register and map the two color channels, the spots representing bleeding through the donor channel to the acceptor channel are used. Finally, correlation analysis and likelihood ratio statistic for the change point detection (CPD) are developed to study the two channels simultaneously, resolve FRET states, and report the dwelling time of each state. The performance of our method has been checked using both simulation and real data.
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Affiliation(s)
- Hao-Chih Lee
- Academia Sinica, Institute of Statistical Science, Taipei, Taiwan
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74
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Bockenhauer S, Fürstenberg A, Yao XJ, Kobilka BK, Moerner WE. Conformational dynamics of single G protein-coupled receptors in solution. J Phys Chem B 2011; 115:13328-38. [PMID: 21928818 DOI: 10.1021/jp204843r] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G protein-coupled receptors (GPCRs) comprise a large family of seven-helix transmembrane proteins which regulate cellular signaling by sensing light, ligands, and binding proteins. The GPCR activation process, however, is not a simple on-off switch; current models suggest a complex conformational landscape in which the active, signaling state includes multiple conformations with similar downstream activity. The present study probes the conformational dynamics of single β(2)-adrenergic receptors (β(2)ARs) in the solution phase by Anti-Brownian ELectrokinetic (ABEL) trapping. The ABEL trap uses fast electrokinetic feedback in a microfluidic configuration to allow direct observation of a single fluorescently labeled β(2)AR for hundreds of milliseconds to seconds. By choosing a reporter dye and labeling site sensitive to ligand binding, we observe a diversity of discrete fluorescence intensity and lifetime levels in single β(2)ARs, indicating a varying radiative lifetime and a range of discrete conformational states with dwell times of hundreds of milliseconds. We find that the binding of agonist increases the dwell times of these states, and furthermore, we observe millisecond fluctuations within states. The intensity autocorrelations of these faster fluctuations are well-described by stretched exponential functions with a stretching exponent β ~ 0.5, suggesting protein dynamics over a range of time scales.
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Affiliation(s)
- Samuel Bockenhauer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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75
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Redox cycling and kinetic analysis of single molecules of solution-phase nitrite reductase. Proc Natl Acad Sci U S A 2011; 108:17269-74. [PMID: 21969548 DOI: 10.1073/pnas.1113572108] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule measurements are a valuable tool for revealing details of enzyme mechanisms by enabling observation of unsynchronized behavior. However, this approach often requires immobilizing the enzyme on a substrate, a process which may alter enzyme behavior. We apply a microfluidic trapping device to allow, for the first time, prolonged solution-phase measurement of single enzymes in solution. Individual redox events are observed for single molecules of a blue nitrite reductase and are used to extract the microscopic kinetic parameters of the proposed catalytic cycle. Changes in parameters as a function of substrate concentration are consistent with a random sequential substrate binding mechanism.
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76
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77
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Sensing cooperativity in ATP hydrolysis for single multisubunit enzymes in solution. Proc Natl Acad Sci U S A 2011; 108:16962-7. [PMID: 21896715 DOI: 10.1073/pnas.1112244108] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In order to operate in a coordinated fashion, multisubunit enzymes use cooperative interactions intrinsic to their enzymatic cycle, but this process remains poorly understood. Accordingly, ATP number distributions in various hydrolyzed states have been obtained for single copies of the mammalian double-ring multisubunit chaperonin TRiC/CCT in free solution using the emission from chaperonin-bound fluorescent nucleotides and closed-loop feedback trapping provided by an Anti-Brownian ELectrokinetic trap. Observations of the 16-subunit complexes as ADP molecules are dissociating shows a peak in the bound ADP number distribution at 8 ADP, whose height falls over time with little shift in the position of the peak, indicating a highly cooperative ADP release process which would be difficult to observe by ensemble-averaged methods. When AlFx is added to produce ATP hydrolysis transition state mimics (ADP·AlFx) locked to the complex, the peak at 8 nucleotides dominates for all but the lowest incubation concentrations. Although ensemble averages of the single-molecule data show agreement with standard cooperativity models, surprisingly, the observed number distributions depart from standard models, illustrating the value of these single-molecule observations in constraining the mechanism of cooperativity. While a complete alternative microscopic model cannot be defined at present, the addition of subunit-occupancy-dependent cooperativity in hydrolysis yields distributions consistent with the data.
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78
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Vasdekis AE, Laporte GP. Enhancing single molecule imaging in optofluidics and microfluidics. Int J Mol Sci 2011; 12:5135-56. [PMID: 21954349 PMCID: PMC3179156 DOI: 10.3390/ijms12085135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/23/2011] [Accepted: 07/25/2011] [Indexed: 12/25/2022] Open
Abstract
Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.
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Affiliation(s)
- Andreas E. Vasdekis
- Optics Laboratory, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; E-Mail:
| | - Gregoire P.J. Laporte
- Optics Laboratory, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; E-Mail:
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79
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Wang Q, Moerner WE. An Adaptive Anti-Brownian ELectrokinetic trap with real-time information on single-molecule diffusivity and mobility. ACS NANO 2011; 5:5792-5799. [PMID: 21612271 DOI: 10.1021/nn2014968] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present the design and implementation of an adaptive Anti-Brownian ELectrokinetic (ABEL) trap capable of extracting estimates of the diffusion coefficient and mobility of single trapped fluorescent nanoscale objects such as biomolecules in solution. The system features rapid acousto-optic scanning of a confocal excitation spot on a 2D square lattice to encode position information on the arrival time of each detected photon, and Kalman filter-based signal processing unit for refined position estimation. We demonstrate stable trapping of multisubunit proteins (D ≈ 22 μm(2)/s) with a count rate of 6 kHz for as long as 15 s and small single-stranded DNA molecules (D ≈ 118 μm(2)/s) at a 15 kHz count rate for seconds. Moreover, we demonstrate real-time measurement of diffusion coefficient and electrokinetic mobility of trapped objects, using adaptive tuning of the Kalman filter parameters.
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Affiliation(s)
- Quan Wang
- Department of Chemistry, Stanford University, Mail Code 5080, Stanford, California 94305-5080, USA
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80
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Abstract
We experimentally demonstrate the feasibility of an aqueous Paul trap using a proof-of-principle planar device. Radio frequency voltages are used to generate an alternating focusing/defocusing potential well in two orthogonal directions. Individual charged particles are dynamically confined into nanometer scale in space. Compared with conventional Paul traps working in frictionless vacuum, the aqueous environment associated with damping forces and thermally induced fluctuations (Brownian noise) exerts a fundamental influence on the underlying physics. We investigate the impact of these two effects on the confining dynamics, with the aim to reduce the rms value of the positional fluctuations. We find that the rms fluctuations can be modulated by adjusting the voltages and frequencies. This technique provides an alternative for the localization and control of charged particles in an aqueous environment.
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81
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Jankowiak R, Reppert M, Zazubovich V, Pieper J, Reinot T. Site Selective and Single Complex Laser-Based Spectroscopies: A Window on Excited State Electronic Structure, Excitation Energy Transfer, and Electron–Phonon Coupling of Selected Photosynthetic Complexes. Chem Rev 2011; 111:4546-98. [DOI: 10.1021/cr100234j] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mike Reppert
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal H4B1R6 Quebec, Canada
| | - Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University of Berlin, Germany
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | - Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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82
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Abstract
Anti-Brownian electrokinetic traps have been used to trap and study the free-solution dynamics of large protein complexes and long chains of DNA. Small molecules in solution have thus far proved too mobile to trap by any means. Here we explore the ultimate limits on trapping single molecules. We developed a feedback-based anti-Brownian electrokinetic trap in which classical thermal noise is compensated to the maximal extent allowed by quantum measurement noise. We trapped single fluorophores with a molecular weight of < 1 kDa and a hydrodynamic radius of 6.7 Å for longer than one second, in aqueous buffer at room temperature. This achievement represents an 800-fold decrease in the mass of objects trapped in solution, and opens the possibility to trap and manipulate any soluble molecule that can be fluorescently labeled. To illustrate the use of this trap, we studied the binding of unlabeled RecA to fluorescently labeled single-stranded DNA. Binding of RecA induced changes in the DNA diffusion coefficient, electrophoretic mobility, and brightness, all of which were measured simultaneously and on a molecule-by-molecule basis. This device greatly extends the size range of molecules that can be studied by room temperature feedback trapping, and opens the door to further studies of the binding of unmodified proteins to DNA in free solution.
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83
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Krüger TPJ, Ilioaia C, van Grondelle R. Fluorescence Intermittency from the Main Plant Light-Harvesting Complex: Resolving Shifts between Intensity Levels. J Phys Chem B 2011; 115:5071-82. [DOI: 10.1021/jp201609c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tjaart P. J. Krüger
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Cristian Ilioaia
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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84
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Krüger TPJ, Ilioaia C, Valkunas L, van Grondelle R. Fluorescence Intermittency from the Main Plant Light-Harvesting Complex: Sensitivity to the Local Environment. J Phys Chem B 2011; 115:5083-95. [DOI: 10.1021/jp109833x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tjaart P. J. Krüger
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Cristian Ilioaia
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Leonas Valkunas
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300 Vilnius, Lithuania and Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9, LT-10222 Vilnius, Lithuania
| | - Rienk van Grondelle
- Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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85
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Börsch M, Wrachtrup J. Improving FRET‐Based Monitoring of Single Chemomechanical Rotary Motors at Work. Chemphyschem 2011; 12:542-53. [DOI: 10.1002/cphc.201000702] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 12/12/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Michael Börsch
- 3rd Institute of Physics and Stuttgart Research Center SCOPE, University of Stuttgart, Pfaffenwaldring 57, Fax: (+49) 711‐685‐65281
| | - Jörg Wrachtrup
- 3rd Institute of Physics and Stuttgart Research Center SCOPE, University of Stuttgart, Pfaffenwaldring 57, Fax: (+49) 711‐685‐65281
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86
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Taylor JN, Landes CF. Improved resolution of complex single-molecule FRET systems via wavelet shrinkage. J Phys Chem B 2011; 115:1105-14. [PMID: 21214275 DOI: 10.1021/jp1050707] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The resolution of complex interactions found in single-molecule fluorescence resonance energy transfer (smFRET) experiments is hindered by noise. Wavelet shrinkage is proven to reduce noise, but traditional methods introduce artifacts when acting on discontinuous signals, such as those acquired in smFRET experiments. Modifications to the basic method that are specific to smFRET are developed and tested on simulated systems. Use of the Haar wavelet basis produces the most optimally denoised estimates. We also assess various thresholding methods, develop a time-localized noise estimator, and implement a translation-invariant wavelet transformation to reduce artifacts associated with discontinuities and inadequate distinction of noise. The time-local estimator enhances noise reduction by 5-20%, and translation-invariant transformation nearly eliminates the aforementioned artifacts. Kinetic parameters extracted from denoised estimates are accurate to within 5% of the simulated values. Overall, the improved resolution results in the complete and accurate characterization of both simple and complex smFRET systems.
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Affiliation(s)
- J Nick Taylor
- Department of Chemistry, Rice University, Houston, Texas 77251-1892, USA
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87
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Riley EA, Bingham C, Bott ED, Kahr B, Reid PJ. Two mechanisms for fluorescence intermittency of single violamine R molecules. Phys Chem Chem Phys 2011; 13:1879-87. [DOI: 10.1039/c0cp01716g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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88
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Bott ED, Riley EA, Kahr B, Reid PJ. Unraveling the Dispersed Kinetics of Dichlorofluorescein in Potassium Hydrogen Phthalate Crystals. J Phys Chem A 2010; 114:7331-7. [DOI: 10.1021/jp102194u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Eric D. Bott
- Department of Chemistry, University of Washington, Seattle, Washington 98195, and Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003
| | - Erin A. Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, and Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003
| | - Bart Kahr
- Department of Chemistry, University of Washington, Seattle, Washington 98195, and Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003
| | - Philip J. Reid
- Department of Chemistry, University of Washington, Seattle, Washington 98195, and Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003
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