1
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Chu J, Ejaz A, Lin KM, Joseph MR, Coraor AE, Drummond DA, Squires AH. Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels. NATURE NANOTECHNOLOGY 2024; 19:1150-1157. [PMID: 38750166 PMCID: PMC11329371 DOI: 10.1038/s41565-024-01672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Multiplexed, real-time fluorescence detection at the single-molecule level can reveal the stoichiometry, dynamics and interactions of multiple molecular species in mixtures and other complex samples. However, fluorescence-based sensing is typically limited to the detection of just 3-4 colours at a time due to low signal-to-noise ratio, high spectral overlap and the need to maintain the chemical compatibility of dyes. Here we engineered a palette of several dozen composite fluorescent labels, called FRETfluors, for multiplexed spectroscopic measurements at the single-molecule level. FRETfluors are compact nanostructures constructed from three chemical components (DNA, Cy3 and Cy5) with tunable spectroscopic properties due to variations in geometry, fluorophore attachment chemistry and DNA sequence. We demonstrate FRETfluor labelling and detection for low-concentration (<100 fM) mixtures of mRNA, dsDNA and proteins using an anti-Brownian electrokinetic trap. In addition to identifying the unique spectroscopic signature of each FRETfluor, this trap differentiates FRETfluors attached to a target from unbound FRETfluors, enabling wash-free sensing. Although usually considered an undesirable complication of fluorescence, here the inherent sensitivity of fluorophores to the local physicochemical environment provides a new design axis complementary to changing the FRET efficiency. As a result, the number of distinguishable FRETfluor labels can be combinatorically increased while chemical compatibility is maintained, expanding prospects for spectroscopic multiplexing at the single-molecule level using a minimal set of chemical building blocks.
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Affiliation(s)
- Jiachong Chu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Ayesha Ejaz
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Interdisicplinary Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Madeline R Joseph
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Aria E Coraor
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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2
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Foote A, Ishii K, Cullinane B, Tahara T, Goldsmith RH. Quantifying Microsecond Solution-Phase Conformational Dynamics of a DNA Hairpin at the Single-Molecule Level. ACS PHYSICAL CHEMISTRY AU 2024; 4:408-419. [PMID: 39069982 PMCID: PMC11274281 DOI: 10.1021/acsphyschemau.3c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 07/30/2024]
Abstract
Quantifying the rapid conformational dynamics of biological systems is fundamental to understanding the mechanism. However, biomolecules are complex, often containing static and dynamic heterogeneity, thus motivating the use of single-molecule methods, particularly those that can operate in solution. In this study, we measure microsecond conformational dynamics of solution-phase DNA hairpins at the single-molecule level using an anti-Brownian electrokinetic (ABEL) trap. Different conformational states were distinguished by their fluorescence lifetimes, and kinetic parameters describing transitions between these states were determined using two-dimensional fluorescence lifetime correlation (2DFLCS) analysis. Rather than combining fluorescence signals from the entire data set ensemble, long observation times of individual molecules allowed ABEL-2DFLCS to be performed on each molecule independently, yielding the underlying distribution of the system's kinetic parameters. ABEL-2DFLCS on the DNA hairpins resolved an underlying heterogeneity of fluorescence lifetimes and provided signatures of two-state exponential dynamics with rapid (
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Affiliation(s)
- Alexander
K. Foote
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Kunihiko Ishii
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Brendan Cullinane
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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3
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Assefa GT, Botha JL, van Heerden B, Kyeyune F, Krüger TPJ, Gwizdala M. ApcE plays an important role in light-induced excitation energy dissipation in the Synechocystis PCC6803 phycobilisomes. PHOTOSYNTHESIS RESEARCH 2024; 160:17-29. [PMID: 38407779 PMCID: PMC11006782 DOI: 10.1007/s11120-024-01078-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Phycobilisomes (PBs) play an important role in cyanobacterial photosynthesis. They capture light and transfer excitation energy to the photosynthetic reaction centres. PBs are also central to some photoprotective and photoregulatory mechanisms that help sustain photosynthesis under non-optimal conditions. Amongst the mechanisms involved in excitation energy dissipation that are activated in response to excessive illumination is a recently discovered light-induced mechanism that is intrinsic to PBs and has been the least studied. Here, we used single-molecule spectroscopy and developed robust data analysis methods to explore the role of a terminal emitter subunit, ApcE, in this intrinsic, light-induced mechanism. We isolated the PBs from WT Synechocystis PCC 6803 as well as from the ApcE-C190S mutant of this strain and compared the dynamics of their fluorescence emission. PBs isolated from the mutant (i.e., ApcE-C190S-PBs), despite not binding some of the red-shifted pigments in the complex, showed similar global emission dynamics to WT-PBs. However, a detailed analysis of dynamics in the core revealed that the ApcE-C190S-PBs are less likely than WT-PBs to enter quenched states under illumination but still fully capable of doing so. This result points to an important but not exclusive role of the ApcE pigments in the light-induced intrinsic excitation energy dissipation mechanism in PBs.
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Affiliation(s)
- Gonfa Tesfaye Assefa
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Joshua L Botha
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Bertus van Heerden
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| | - Farooq Kyeyune
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Department of Physics, Faculty of Science, Kyambogo University, P.O. Box 1, Kyambogo, Kampala, Uganda
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| | - Michal Gwizdala
- Department of Physics, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
- ICFO - Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, 08860, Spain.
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4
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Seabury AG, Khodabocus AJ, Kogan IM, Hoy GR, DeSalvo GA, Wustholz KL. Blinking characteristics of organic fluorophores for blink-based multiplexing. Commun Chem 2024; 7:18. [PMID: 38280979 PMCID: PMC10821931 DOI: 10.1038/s42004-024-01106-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Single-molecule fluorescence experiments have transformed our understanding of complex materials and biological systems. Whether single molecules are used to report on their nano-environment or provide for localization, understanding their blinking dynamics (i.e., stochastic fluctuations in emission intensity under continuous illumination) is paramount. We recently demonstrated another use for blinking dynamics called blink-based multiplexing (BBM), where individual emitters are classified using a single excitation laser based on blinking dynamics, rather than color. This study elucidates the structure-activity relationships governing BBM performance in a series of model rhodamine, BODIPY, and anthraquinone fluorophores that undergo different photo-physical and-chemical processes during blinking. Change point detection and multinomial logistic regression analyses show that BBM can leverage spectral fluctuations, electron and proton transfer kinetics, as well as photostability for molecular classification-even within the context of a shared blinking mechanism. In doing so, we demonstrate two- and three-color BBM with ≥ 93% accuracy using spectrally-overlapped fluorophores.
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Affiliation(s)
| | | | | | - Grayson R Hoy
- Chemistry Department, William & Mary, Williamsburg, VA, USA
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5
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Tsoraev GV, Protasova EA, Klimanova EA, Ryzhykau YL, Kuklin AI, Semenov YS, Ge B, Li W, Qin S, Friedrich T, Sluchanko NN, Maksimov EG. Anti-Stokes fluorescence excitation reveals conformational mobility of the C-phycocyanin chromophores. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054701. [PMID: 36065339 PMCID: PMC9440762 DOI: 10.1063/4.0000164] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/08/2022] [Indexed: 05/15/2023]
Abstract
The structural organization of natural pigment-protein complexes provides a specific environment for the chromophore groups. Yet, proteins are inherently dynamic and conformationally mobile. In this work, we demonstrate the heterogeneity of chromophores of C-phycocyanin (C-PC) from Arthrospira platensis. Part of the population of trimeric C-PC is subject to spontaneous disturbances of protein-protein interactions resulting in increased conformational mobility of the chromophores. Upon fluorescence excitation in the visible range, the spectral signatures of these poorly populated states are masked by bulk chromophore states, but the former could be clearly discriminated when the fluorescence is excited by near-infrared quanta. Such selective excitation of conformationally mobile C-PC chromophores is due to the structure of their S1 level, which is characterized by a significantly broadened spectral line. We demonstrate that the anti-Stokes C-PC fluorescence is the result of single-photon absorption. By combining spectral and structural methods, we characterize four distinct states of C-PC chromophores emitting at 620, 650, 665, and 720 nm and assigned the fast component in the anti-Stokes fluorescence decay kinetics in the range of 690-750 nm to the chromophores with increased conformational mobility. Our data suggest that the spectral and temporal characteristics of the anti-Stokes fluorescence can be used to study protein dynamics and develop methods to visualize local environment parameters such as temperature.
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Affiliation(s)
- Georgy V. Tsoraev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elena A. Protasova
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | | | | | | | - Yury S. Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Baosheng Ge
- China University of Petroleum (Huadong), College of Chemical Engineering, Qingdao 266580, People's Republic of China
| | - Wenjun Li
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, People's Republic of China
| | | | - Thomas Friedrich
- Technical University of Berlin, Institute of Chemistry PC 14, D-10623 Berlin, Germany
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Author to whom correspondence should be addressed:. Tel.: +7 (926) 735–04-37
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6
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Moya R, Norris AC, Spangler LC, Scholes GD, Schlau-Cohen GS. Observation of conformational dynamics in single light-harvesting proteins from cryptophyte algae. J Chem Phys 2022; 157:035102. [PMID: 35868944 PMCID: PMC9894659 DOI: 10.1063/5.0095763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Photosynthetic organisms use pigment-protein complexes to capture the sunlight that powers most life on earth. Within these complexes, the position of the embedded pigments is all optimized for light harvesting. At the same time, the protein scaffold undergoes thermal fluctuations that vary the structure, and, thus, photophysics, of the complexes. While these variations are averaged out in ensemble measurements, single-molecule spectroscopy provides the ability to probe these conformational changes. We used single-molecule fluorescence spectroscopy to identify the photophysical substates reflective of distinct conformations and the associated conformational dynamics in phycoerythrin 545 (PE545), a pigment-protein complex from cryptophyte algae. Rapid switching between photophysical states was observed, indicating that ensemble measurements average over a conformational equilibrium. A highly quenched conformation was also identified, and its population increased under high light. This discovery establishes that PE545 has the characteristics to serve as a photoprotective site. Finally, unlike homologous proteins from the evolutionarily related cyanobacteria and red algae, quenching was not observed upon photobleaching, which may allow for robust photophysics without the need for rapid repair or replacement machinery. Collectively, these observations establish the presence of a rich and robust set of conformational states of PE545. Cryptophytes exhibit particularly diverse energetics owing to the variety of microenvironments in which they survive, and the conformational states and dynamics reported here may provide photophysical flexibility that contributes to their remarkable ability to flourish under diverse conditions.
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Affiliation(s)
- Raymundo Moya
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Audrey C. Norris
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Leah C. Spangler
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Gregory D. Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA,Author to whom correspondence should be addressed:
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7
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Srinivasan S, Regmi R, Lin X, Dreyer CA, Chen X, Quinn SD, He W, Coleman MA, Carraway KL, Zhang B, Schlau-Cohen GS. Ligand-induced transmembrane conformational coupling in monomeric EGFR. Nat Commun 2022; 13:3709. [PMID: 35794108 PMCID: PMC9259572 DOI: 10.1038/s41467-022-31299-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/13/2022] [Indexed: 01/26/2023] Open
Abstract
Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. This transmembrane signaling is generally initiated by ligand binding to the receptors in their monomeric form. While subsequent receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution of monomeric receptors has been challenging to isolate due to the complexity and ligand-dependence of these interactions. By combining membrane nanodiscs produced with cell-free expression, single-molecule Förster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes upon ligand binding are common to single-pass membrane proteins.
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Affiliation(s)
- Shwetha Srinivasan
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Raju Regmi
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA ,grid.4444.00000 0001 2112 9282Present Address: Institut Curie, CNRS, Laboratoire Physico Chimie Curie, Paris, France
| | - Xingcheng Lin
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Courtney A. Dreyer
- grid.27860.3b0000 0004 1936 9684Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817 USA
| | - Xuyan Chen
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Steven D. Quinn
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA ,grid.5685.e0000 0004 1936 9668Present Address: Department of Physics, University of York, York, UK
| | - Wei He
- grid.250008.f0000 0001 2160 9702Lawrence Livermore National Laboratory, Livermore, CA 94550 USA
| | - Matthew A. Coleman
- grid.250008.f0000 0001 2160 9702Lawrence Livermore National Laboratory, Livermore, CA 94550 USA ,grid.27860.3b0000 0004 1936 9684Radiation Oncology, University of California Davis School of Medicine, Sacramento, CA 95817 USA
| | - Kermit L. Carraway
- grid.27860.3b0000 0004 1936 9684Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, CA 95817 USA
| | - Bin Zhang
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
| | - Gabriela S. Schlau-Cohen
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
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8
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Carpenter W, Lavania AA, Borden JS, Oltrogge LM, Perez D, Dahlberg PD, Savage DF, Moerner WE. Ratiometric Sensing of Redox Environments Inside Individual Carboxysomes Trapped in Solution. J Phys Chem Lett 2022; 13:4455-4462. [PMID: 35549289 PMCID: PMC9150107 DOI: 10.1021/acs.jpclett.2c00782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Diffusion of biological nanoparticles in solution impedes our ability to continuously monitor individual particles and measure their physical and chemical properties. To overcome this, we previously developed the interferometric scattering anti-Brownian electrokinetic (ISABEL) trap, which uses scattering to localize a particle and applies electrokinetic forces that counteract Brownian motion, thus enabling extended observation. Here we present an improved ISABEL trap that incorporates a near-infrared scatter illumination beam and rapidly interleaves 405 and 488 nm fluorescence excitation reporter beams. With the ISABEL trap, we monitored the internal redox environment of individual carboxysomes labeled with the ratiometric redox reporter roGFP2. Carboxysomes widely vary in scattering contrast (reporting on size) and redox-dependent ratiometric fluorescence. Furthermore, we used redox sensing to explore the chemical kinetics within intact carboxysomes, where bulk measurements may contain unwanted contributions from aggregates or interfering fluorescent proteins. Overall, we demonstrate the ISABEL trap's ability to sensitively monitor nanoscale biological objects, enabling new experiments on these systems.
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Affiliation(s)
- William
B. Carpenter
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Julia S. Borden
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National
Accelerator Laboratory, Menlo Park, California 94025, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California Berkeley, Berkeley, California 94720, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
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9
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Sielaff H, Dienerowitz F, Dienerowitz M. Single-molecule FRET combined with electrokinetic trapping reveals real-time enzyme kinetics of individual F-ATP synthases. NANOSCALE 2022; 14:2327-2336. [PMID: 35084006 DOI: 10.1039/d1nr05754e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a key technique to observe conformational changes in molecular motors and to access the details of single-molecule static and dynamic disorder during catalytic processes. However, studying freely diffusing molecules in solution is limited to a few tens of milliseconds, while surface attachment often bears the risk to restrict their natural motion. In this paper we combine smFRET and electrokinetic trapping (ABEL trap) to non-invasively hold single FOF1-ATP synthases for up to 3 s within the detection volume, thereby extending the observation time by a factor of 10 as compared to Brownian diffusion without surface attachment. In addition, we are able to monitor complete reaction cycles and to selectively trap active molecules based on their smFRET signal, thus speeding up the data acquisition process. We demonstrate the capability of our method to study the dynamics of single molecules by recording the ATP-hydrolysis driven rotation of individual FOF1-ATP synthase molecules over numerous reaction cycles and extract their kinetic rates. We argue that our method is not limited to motor proteins. Instead, it can be applied to monitor conformational changes with millisecond time resolution for a wide range of enzymes, thereby making it a versatile tool for studying protein dynamics.
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Affiliation(s)
- Hendrik Sielaff
- Department of Chemistry, Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, 117557 Singapore, Singapore
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2-4, 07743 Jena, Germany.
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10
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Moya R, Norris AC, Kondo T, Schlau-Cohen GS. Observation of robust energy transfer in the photosynthetic protein allophycocyanin using single-molecule pump-probe spectroscopy. Nat Chem 2022; 14:153-159. [PMID: 34992285 PMCID: PMC9977402 DOI: 10.1038/s41557-021-00841-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/20/2021] [Indexed: 01/26/2023]
Abstract
Photosynthetic organisms convert sunlight to electricity with near unity quantum efficiency. Absorbed photoenergy transfers through a network of chromophores positioned within protein scaffolds, which fluctuate due to thermal motion. The resultant variation in the individual energy transfer steps has not yet been measured, and so how the efficiency is robust to this variation has not been determined. Here, we describe single-molecule pump-probe spectroscopy with facile spectral tuning and its application to the ultrafast dynamics of single allophycocyanin, a light-harvesting protein from cyanobacteria. We disentangled the energy transfer and energetic relaxation from nuclear motion using the spectral dependence of the dynamics. We observed an asymmetric distribution of timescales for energy transfer and a slower and more heterogeneous distribution of timescales for energetic relaxation, which was due to the impact of the protein environment. Collectively, these results suggest that energy transfer is robust to protein fluctuations, a prerequisite for efficient light harvesting.
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Affiliation(s)
- Raymundo Moya
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Audrey C. Norris
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Toru Kondo
- Department of Life Science and Technology, Tokyo Institute of Technology,PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA,To whom correspondence should be addressed;
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11
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Squires A, Wang Q, Dahlberg P, Moerner WE. A bottom-up perspective on photodynamics and photoprotection in light-harvesting complexes using anti-Brownian trapping. J Chem Phys 2022; 156:070901. [DOI: 10.1063/5.0079042] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Quan Wang
- Genomics, Princeton University, United States of America
| | | | - W. E. Moerner
- Department of Chemistry, Stanford University, United States of America
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12
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Kondo T, Shibata Y. Recent advances in single-molecule spectroscopy studies on light-harvesting processes in oxygenic photosynthesis. Biophys Physicobiol 2022. [PMCID: PMC9173860 DOI: 10.2142/biophysico.bppb-v19.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Photosynthetic light-harvesting complexes (LHCs) play a crucial role in concentrating the photon energy from the sun that otherwise excites a typical pigment molecule, such as chlorophyll-a, only several times a second. Densely packed pigments in the complexes ensure efficient energy transfer to the reaction center. At the same time, LHCs have the ability to switch to an energy-quenching state and thus play a photoprotective role under excessive light conditions. Photoprotection is especially important for oxygenic photosynthetic organisms because toxic reactive oxygen species can be generated through photochemistry under aerobic conditions. Because of the extreme complexity of the systems in which various types of pigment molecules strongly interact with each other and with the surrounding protein matrixes, there has been long-standing difficulty in understanding the molecular mechanisms underlying the flexible switching between the light-harvesting and quenching states. Single-molecule spectroscopy studies are suitable to reveal the conformational dynamics of LHCs reflected in the fluorescence properties that are obscured in ordinary ensemble measurements. Recent advanced single-molecule spectroscopy studies have revealed the dynamical fluctuations of LHCs in their fluorescence peak position, intensity, and lifetime. The observed dynamics seem relevant to the conformational plasticity required for the flexible activations of photoprotective energy quenching. In this review, we survey recent advances in the single-molecule spectroscopy study of the light-harvesting systems of oxygenic photosynthesis.
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Affiliation(s)
- Toru Kondo
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Yutaka Shibata
- Department of Chemistry, Graduate School of Science, Tohoku University
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13
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Talele S, King JT. Fast and robust two-dimensional inverse Laplace transformation of single-molecule fluorescence lifetime data. Biophys J 2021; 120:4590-4599. [PMID: 34461104 DOI: 10.1016/j.bpj.2021.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/08/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022] Open
Abstract
Fluorescence spectroscopy at the single-molecule scale has been indispensable for studying conformational dynamics and rare states of biological macromolecules. Single-molecule two-dimensional (2D) fluorescence lifetime correlation spectroscopy is an emerging technique that holds promise for the study of protein and nucleic acid dynamics, as the technique is 1) capable of resolving conformational dynamics using a single chromophore, 2) resolves forward and reverse transitions independently, and 3) has a dynamic window ranging from microseconds to seconds. However, the calculation of a 2D fluorescence relaxation spectrum requires an inverse Laplace transform (ILT), which is an ill-conditioned inversion that must be estimated numerically through a regularized minimization. Current methods for performing ILTs of fluorescence relaxation can be computationally inefficient, sensitive to noise corruption, and difficult to implement. Here, we adopt an approach developed for NMR spectroscopy (T1-T2 relaxometry) to perform one-dimensional (1D) and 2D-ILTs on single-molecule fluorescence spectroscopy data using singular-valued decomposition and Tikhonov regularization. This approach provides fast, robust, and easy to implement Laplace inversions of single-molecule fluorescence data. We compare this approach to the widely used maximal entropy method.
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Affiliation(s)
- Saurabh Talele
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - John T King
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, Republic of Korea.
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14
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Wang B, Davis LM. Diffusivity Measurement by Single-Molecule Recycling in a Capillary Microchannel. MICROMACHINES 2021; 12:800. [PMID: 34357210 PMCID: PMC8306395 DOI: 10.3390/mi12070800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/04/2021] [Indexed: 11/16/2022]
Abstract
Microfluidic devices have been extensively investigated in recent years in fields including ligand-binding analysis, chromatographic separation, molecular dynamics, and DNA sequencing. To prolong the observation of a single molecule in aqueous buffer, the solution in a sub-micron scale channel is driven by a electric field and reversed after a fixed delay following each passage, so that the molecule passes back and forth through the laser focus and the time before irreversible photobleaching is extended. However, this practice requires complex chemical treatment to the inner surface of the channel to prevent unexpected sticking to the surface and the confined space renders features, such as a higher viscosity and lower dielectric constant, which slow the Brownian motion of the molecule compared to the bulk solution. Additionally, electron beam lithography used for the fabrication of the nanochannel substantially increases the cost, and the sub-micron dimensions make the molecule difficult to locate. In this paper, we propose a method of single-molecule recycling in a capillary microchannel. A commercial fused-silica capillary with an inner diameter of 2 microns is chopped into a 1-inch piece and is fixed onto a cover slip. Two o-rings on the sides used as reservoirs and an o-ring in the middle used as observation window are glued over the capillary. The inner surface of the capillary is chemically processed to reduce the non-specific sticking and to improve capillary effect. The device does not require high-precision fabrication and thus is less costly and easier to prepare than the nanochannel. 40 nm Fluospheres® in 50% methanol are used as working solution. The capillary is translated by a piezo stage to recycle the molecule, which diffuses freely through the capillary, and a confocal microscope is used for fluorescence collection. The passing times of the molecule through the laser focus are calculated by a real-time control system based on an FPGA, and the commands of translation are given to the piezo stage through a feedback algorithm. The larger dimensions of the capillary overcomes the strong sticking, the reduced diffusivity, and the difficulty of localizing the molecule. We have achieved a maximum number of recycles of more than 200 and developed a maximum-likelihood estimation of the diffusivity of the molecule, which attains results of the same magnitude as the previous report. This technique simplifies the overall procedure of the single-molecule recycling and could be useful for the ligand-binding studies in high-throughput screening.
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Affiliation(s)
- Bo Wang
- Center for Laser Application, University of Tennessee Space Institute, 411 B H Goethert Pkwy, Tullahoma, TN 37388, USA
- Department of Physics and Astronomy, University of Tennessee Knoxville, 1408 Circle Dr, Knoxville, TN 37996, USA;
| | - Lloyd M. Davis
- Center for Laser Application, University of Tennessee Space Institute, 411 B H Goethert Pkwy, Tullahoma, TN 37388, USA
- Department of Physics and Astronomy, University of Tennessee Knoxville, 1408 Circle Dr, Knoxville, TN 37996, USA;
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15
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Dienerowitz M, Howard JAL, Quinn SD, Dienerowitz F, Leake MC. Single-molecule FRET dynamics of molecular motors in an ABEL trap. Methods 2021; 193:96-106. [PMID: 33571667 DOI: 10.1016/j.ymeth.2021.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/22/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Single-molecule Förster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key challenge of such FRET investigations is to observe a molecule in action for long enough without restricting its natural function. The Anti-Brownian ELectrokinetic Trap (ABEL trap) sets out to combine smFRET with molecular confinement to enable observation times of up to several seconds while removing any requirement of tethered surface attachment of the molecule in question. In addition, the ABEL trap's inherent ability to selectively capture FRET active molecules accelerates the data acquisition process. In this work we exemplify the capabilities of the ABEL trap in performing extended timescale smFRET measurements on the molecular motor Rep, which is crucial for removing protein blocks ahead of the advancing DNA replication machinery and for restarting stalled DNA replication. We are able to monitor single Rep molecules up to 6 seconds with sub-millisecond time resolution capturing multiple conformational switching events during the observation time. Here we provide a step-by-step guide for the rational design, construction and implementation of the ABEL trap for smFRET detection of Rep in vitro. We include details of how to model the electric potential at the trap site and use Hidden Markov analysis of the smFRET trajectories.
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Affiliation(s)
- Maria Dienerowitz
- Single-Molecule Microscopy Group, Universitätsklinikum Jena, Nonnenplan 2 - 4, 07743 Jena, Germany.
| | - Jamieson A L Howard
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Steven D Quinn
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Frank Dienerowitz
- Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Mark C Leake
- Department of Physics, University of York, Heslington, York YO10 5DD, UK; Department of Biology, University of York, Heslington, York YO10 5DD, UK; York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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16
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Abstract
To date, single molecule studies have been reliant on tethering or confinement to achieve long duration and high temporal resolution measurements. Here, we present a 3D single-molecule active real-time tracking method (3D-SMART) which is capable of locking on to single fluorophores in solution for minutes at a time with photon limited temporal resolution. As a demonstration, 3D-SMART is applied to actively track single Atto 647 N fluorophores in 90% glycerol solution with an average duration of ~16 s at count rates of ~10 kHz. Active feedback tracking is further applied to single proteins and nucleic acids, directly measuring the diffusion of various lengths (99 to 1385 bp) of single DNA molecules at rates up to 10 µm2/s. In addition, 3D-SMART is able to quantify the occupancy of single Spinach2 RNA aptamers and capture active transcription on single freely diffusing DNA. 3D-SMART represents a critical step towards the untethering of single molecule spectroscopy. Single molecule observation has been limited to tethered molecules to ensure that the target remains in the field of view (FOV). Here, the authors develop a real-time tracking method that locks onto rapidly diffusing targets and tracks them in a 3D volume, enabling single molecules to remain in the FOV for minutes at a time.
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17
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Willems K, Ruić D, Biesemans A, Galenkamp NS, Van Dorpe P, Maglia G. Engineering and Modeling the Electrophoretic Trapping of a Single Protein Inside a Nanopore. ACS NANO 2019; 13:9980-9992. [PMID: 31403770 PMCID: PMC6764111 DOI: 10.1021/acsnano.8b09137] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ability to confine and to study single molecules has enabled important advances in natural and applied sciences. Recently, we have shown that unlabeled proteins can be confined inside the biological nanopore Cytolysin A (ClyA) and conformational changes monitored by ionic current recordings. However, trapping small proteins remains a challenge. Here, we describe a system where steric, electrostatic, electrophoretic, and electro-osmotic forces are exploited to immobilize a small protein, dihydrofolate reductase (DHFR), inside ClyA. Assisted by electrostatic simulations, we show that the dwell time of DHFR inside ClyA can be increased by orders of magnitude (from milliseconds to seconds) by manipulation of the DHFR charge distribution. Further, we describe a physical model that includes a double energy barrier and the main electrophoretic components for trapping DHFR inside the nanopore. Simultaneous fits to the voltage dependence of the dwell times allowed direct estimates of the cis and trans translocation probabilities, the mean dwell time, and the force exerted by the electro-osmotic flow on the protein (≅9 pN at -50 mV) to be retrieved. The observed binding of NADPH to the trapped DHFR molecules suggested that the engineered proteins remained folded and functional inside ClyA. Contact-free confinement of single proteins inside nanopores can be employed for the manipulation and localized delivery of individual proteins and will have further applications in single-molecule analyte sensing and enzymology studies.
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Affiliation(s)
- Kherim Willems
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
| | - Dino Ruić
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Annemie Biesemans
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Nicole Stéphanie Galenkamp
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pol Van Dorpe
- imec, Kapeldreef 75, B-3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- E-mail:
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18
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Real-Time 3D Single Particle Tracking: Towards Active Feedback Single Molecule Spectroscopy in Live Cells. Molecules 2019; 24:molecules24152826. [PMID: 31382495 PMCID: PMC6695621 DOI: 10.3390/molecules24152826] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/27/2019] [Accepted: 08/01/2019] [Indexed: 01/25/2023] Open
Abstract
Single molecule fluorescence spectroscopy has been largely implemented using methods which require tethering of molecules to a substrate in order to make high temporal resolution measurements. However, the act of tethering a molecule requires that the molecule be removed from its environment. This is especially perturbative when measuring biomolecules such as enzymes, which may rely on the non-equilibrium and crowded cellular environment for normal function. A method which may be able to un-tether single molecule fluorescence spectroscopy is real-time 3D single particle tracking (RT-3D-SPT). RT-3D-SPT uses active feedback to effectively lock-on to freely diffusing particles so they can be measured continuously with up to photon-limited temporal resolution over large axial ranges. This review gives an overview of the various active feedback 3D single particle tracking methods, highlighting specialized detection and excitation schemes which enable high-speed real-time tracking. Furthermore, the combination of these active feedback methods with simultaneous live-cell imaging is discussed. Finally, the successes in real-time 3D single molecule tracking (RT-3D-SMT) thus far and the roadmap going forward for this promising family of techniques are discussed.
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19
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Atallah TL, Sica AV, Shin AJ, Friedman HC, Kahrobai YK, Caram JR. Decay-Associated Fourier Spectroscopy: Visible to Shortwave Infrared Time-Resolved Photoluminescence Spectra. J Phys Chem A 2019; 123:6792-6798. [DOI: 10.1021/acs.jpca.9b04924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Timothy L. Atallah
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Anthony V. Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Ashley J. Shin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Hannah C. Friedman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Yaniv K. Kahrobai
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Justin R. Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
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20
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Squires A, Lavania AA, Dahlberg PD, Moerner WE. Interferometric Scattering Enables Fluorescence-Free Electrokinetic Trapping of Single Nanoparticles in Free Solution. NANO LETTERS 2019; 19:4112-4117. [PMID: 31117762 PMCID: PMC6604838 DOI: 10.1021/acs.nanolett.9b01514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/13/2019] [Indexed: 05/05/2023]
Abstract
Anti-Brownian traps confine single particles in free solution by closed-loop feedback forces that directly counteract Brownian motion. Extended-duration measurements on trapped objects allow detailed characterization of photophysical and transport properties as well as observation of infrequent or rare dynamics. However, this approach has been generally limited to particles that can be tracked by fluorescence emission. Here we present the Interferometric Scattering Anti-Brownian ELectrokinetic (ISABEL) trap, which uses interferometric scattering rather than fluorescence to monitor particle position. By decoupling the ability to track (and therefore trap) a particle from collection of its spectroscopic data, the ISABEL trap enables confinement and extended study of single particles that do not fluoresce, only weakly fluoresce, or exhibit intermittent fluorescence or photobleaching. This new technique significantly expands the range of nanoscale objects that may be investigated at the single-particle level in free solution.
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Affiliation(s)
- Allison
H. Squires
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Abhijit A. Lavania
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Applied Physics, Stanford University, Stanford, California 94305, United States
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21
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Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy. Proc Natl Acad Sci U S A 2019; 116:11247-11252. [PMID: 31101718 DOI: 10.1073/pnas.1821207116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is essential for survival. Protein dynamics are often local conformational changes, which allows multiple dynamical processes to occur simultaneously and rapidly in individual proteins. Experiments often average over these dynamics and their multiplicity, preventing identification of the molecular origin and impact on biological function. Green plants survive under high light by quenching excess energy, and Light-Harvesting Complex Stress Related 1 (LHCSR1) is the protein responsible for quenching in moss. Here, we expand an analysis of the correlation function of the fluorescence lifetime by improving the estimation of the lifetime states and by developing a multicomponent model correlation function, and we apply this analysis at the single-molecule level. Through these advances, we resolve previously hidden rapid dynamics, including multiple parallel processes. By applying this technique to LHCSR1, we identify and quantitate parallel dynamics on hundreds of microseconds and tens of milliseconds timescales, likely at two quenching sites within the protein. These sites are individually controlled in response to fluctuations in sunlight, which provides robust regulation of the light-harvesting machinery. Considering our results in combination with previous structural, spectroscopic, and computational data, we propose specific pigments that serve as the quenching sites. These findings, therefore, provide a mechanistic basis for quenching, illustrating the ability of this method to uncover protein function.
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22
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Squires AH, Dahlberg PD, Liu H, Magdaong NCM, Blankenship RE, Moerner WE. Single-molecule trapping and spectroscopy reveals photophysical heterogeneity of phycobilisomes quenched by Orange Carotenoid Protein. Nat Commun 2019; 10:1172. [PMID: 30862823 PMCID: PMC6414729 DOI: 10.1038/s41467-019-09084-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
The Orange Carotenoid Protein (OCP) is a cytosolic photosensor that is responsible for non-photochemical quenching (NPQ) of the light-harvesting process in most cyanobacteria. Upon photoactivation by blue-green light, OCP binds to the phycobilisome antenna complex, providing an excitonic trap to thermally dissipate excess energy. At present, both the binding site and NPQ mechanism of OCP are unknown. Using an Anti-Brownian ELectrokinetic (ABEL) trap, we isolate single phycobilisomes in free solution, both in the presence and absence of activated OCP, to directly determine the photophysics and heterogeneity of OCP-quenched phycobilisomes. Surprisingly, we observe two distinct OCP-quenched states, with lifetimes 0.09 ns (6% of unquenched brightness) and 0.21 ns (11% brightness). Photon-by-photon Monte Carlo simulations of exciton transfer through the phycobilisome suggest that the observed quenched states are kinetically consistent with either two or one bound OCPs, respectively, underscoring an additional mechanism for excitation control in this key photosynthetic unit. Upon photoactivation the Orange Carotenoid Protein (OCP) binds to the phycobilisome and prevents damage by thermally dissipating excess energy. Here authors use an Anti-Brownian ELectrokinetic trap to determine the photophysics of single OCP-quenched phycobilisomes and observe two distinct OCP-quenched states with either one or two OCPs bound.
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Affiliation(s)
- Allison H Squires
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Haijun Liu
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Nikki Cecil M Magdaong
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
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23
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Sielaff H, Yanagisawa S, Frasch WD, Junge W, Börsch M. Structural Asymmetry and Kinetic Limping of Single Rotary F-ATP Synthases. Molecules 2019; 24:E504. [PMID: 30704145 PMCID: PMC6384691 DOI: 10.3390/molecules24030504] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
F-ATP synthases use proton flow through the FO domain to synthesize ATP in the F₁ domain. In Escherichia coli, the enzyme consists of rotor subunits γεc10 and stator subunits (αβ)₃δab₂. Subunits c10 or (αβ)₃ alone are rotationally symmetric. However, symmetry is broken by the b₂ homodimer, which together with subunit δa, forms a single eccentric stalk connecting the membrane embedded FO domain with the soluble F₁ domain, and the central rotating and curved stalk composed of subunit γε. Although each of the three catalytic binding sites in (αβ)₃ catalyzes the same set of partial reactions in the time average, they might not be fully equivalent at any moment, because the structural symmetry is broken by contact with b₂δ in F₁ and with b₂a in FO. We monitored the enzyme's rotary progression during ATP hydrolysis by three single-molecule techniques: fluorescence video-microscopy with attached actin filaments, Förster resonance energy transfer between pairs of fluorescence probes, and a polarization assay using gold nanorods. We found that one dwell in the three-stepped rotary progression lasting longer than the other two by a factor of up to 1.6. This effect of the structural asymmetry is small due to the internal elastic coupling.
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Affiliation(s)
- Hendrik Sielaff
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
| | - Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wayne D Frasch
- School of Life Sciences, Arizona State University, Tempe, Arizona, AZ 85287, USA.
| | - Wolfgang Junge
- Department of Biology & Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University, 07743 Jena, Germany.
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24
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Foote AK, Manger LH, Holden MR, Margittai M, Goldsmith RH. Time-resolved multirotational dynamics of single solution-phase tau proteins reveals details of conformational variation. Phys Chem Chem Phys 2019; 21:1863-1871. [PMID: 30632561 PMCID: PMC6449148 DOI: 10.1039/c8cp06971a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Intrinsically disordered proteins (IDPs) are crucial to many cellular processes and have been linked to neurodegenerative diseases. Single molecules of tau, an IDP associated with Alzheimer's disease, are trapped in solution using a microfluidic device, and a time-resolved fluorescence anisotropy decay is recorded for each molecule. Multiple rotational components are resolved and a novel k-means algorithm is used to sort the molecules into two families of conformations. Differences in rotational dynamics suggest a change in the rigidity and steric hindrance surrounding a sequence (306VQIVYK311) which is central to paired helical filament formation. This single-molecule approach can be applied to other IDPs to resolve heterogeneous populations and underlying differences in conformational dynamics.
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Affiliation(s)
- Alexander K Foote
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706, USA.
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25
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Abstract
Time series obtained from time-dependent experiments contain rich information on kinetics and dynamics of the system under investigation. This work describes an unsupervised learning framework, along with the derivation of the necessary analytical expressions, for the analysis of Gaussian-distributed time series that exhibit discrete states. After the time series has been partitioned into segments in a model-free manner using the previously developed change-point (CP) method, this protocol starts with an agglomerative hierarchical clustering algorithm to classify the detected segments into possible states. The initial state clustering is further refined using an expectation-maximization (EM) procedure, and the number of states is determined by a Bayesian information criterion (BIC). Also introduced here is an achievement scalarization function, usually seen in artificial intelligence literature, for quantitatively assessing the performance of state determination. The statistical learning framework, which is comprised of three stages, detection of signal change, clustering, and number-of-state determination, was thoroughly characterized using simulated trajectories with random intensity segments that have no underlying kinetics, and its performance was critically evaluated. The application to experimental data is also demonstrated. The results suggested that this general framework, the implementation of which is based on firm theoretical foundations and does not require the imposition of any kinetics model, is powerful in determining the number of states, the parameters contained in each state, as well as the associated statistical significance.
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Affiliation(s)
- Hao Li
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Haw Yang
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
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26
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Radioprotective role of cyanobacterial phycobilisomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:121-128. [PMID: 30465750 DOI: 10.1016/j.bbabio.2018.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/07/2018] [Accepted: 11/18/2018] [Indexed: 11/20/2022]
Abstract
Cyanobacteria are thought to be responsible for pioneering dioxygen production and the so-called "Great Oxygenation Event" that determined the formation of the ozone layer and the ionosphere restricting ionizing radiation levels reaching our planet, which increased biological diversity but also abolished the necessity of radioprotection. We speculated that ancient protection mechanisms could still be present in cyanobacteria and studied the effect of ionizing radiation and space flight during the Foton-M4 mission on Synechocystis sp. PCC6803. Spectral and functional characteristics of photosynthetic membranes revealed numerous similarities of the effects of α-particles and space flight, which both interrupted excitation energy transfer from phycobilisomes to the photosystems and significantly reduced the concentration of phycobiliproteins. Although photosynthetic activity was severely suppressed, the effect was reversible, and the cells could rapidly recover from the stress. We suggest that the actual existence and the uncoupling of phycobilisomes may play a specific role not only in photo-, but also in radioprotection, which could be crucial for the early evolution of Life on Earth.
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27
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Eberle P, Höller C, Müller P, Suomalainen M, Greber UF, Eghlidi H, Poulikakos D. Single entity resolution valving of nanoscopic species in liquids. NATURE NANOTECHNOLOGY 2018; 13:578-582. [PMID: 29784963 DOI: 10.1038/s41565-018-0150-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Investigating biological and synthetic nanoscopic species in liquids, at the ultimate resolution of single entity, is important in diverse fields1-5. Progress has been made6-10, but significant barriers need to be overcome such as the need for intense fields, the lack of versatility in operating conditions and the limited functionality in solutions of high ionic strength for biological applications. Here, we demonstrate switchable electrokinetic nanovalving able to confine and guide single nano-objects, including macromolecules, with sizes down to around 10 nanometres, in a lab-on-chip environment. The nanovalves are based on spatiotemporal tailoring of the potential energy landscape of nano-objects using an electric field, modulated collaboratively by wall nanotopography and by embedded electrodes in a nanochannel system. We combine nanovalves to isolate single entities from an ensemble, and demonstrate their guiding, confining, releasing and sorting. We show on-demand motion control of single immunoglobulin G molecules, quantum dots, adenoviruses, lipid vesicles, dielectric and metallic particles, suspended in electrolytes with a broad range of ionic strengths, up to biological levels. Such systems can enable nanofluidic, large-scale integration and individual handling of multiple entities in applications ranging from single species characterization and screening to in situ chemical or biochemical synthesis in continuous on-chip processes.
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Affiliation(s)
- Patric Eberle
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland
| | - Christian Höller
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland
| | - Philipp Müller
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland
| | - Maarit Suomalainen
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Urs F Greber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Hadi Eghlidi
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland.
| | - Dimos Poulikakos
- Laboratory of Thermodynamics in Emerging Technologies, ETH Zurich, Zurich, Switzerland.
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Das G, Chattoraj S, Nandi S, Mondal P, Saha A, Bhattacharyya K, Ghosh S. Probing the conformational dynamics of photosystem I in unconfined and confined spaces. Phys Chem Chem Phys 2018; 20:449-455. [DOI: 10.1039/c7cp07375e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PSI demonstrates strong fluctuations in fluorescence intensity and lifetime with two conformational states in bulk-water in contrast to a liposome.
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Affiliation(s)
- Gaurav Das
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Shyamtanu Chattoraj
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Somen Nandi
- Department of Physical Chemistry
- Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Prasenjit Mondal
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Abhijit Saha
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Kankan Bhattacharyya
- Department of Chemistry
- Indian Institute of Science Education & Research Bhopal
- Bhopal Bypass Road
- Bhopal-462 066
- India
| | - Surajit Ghosh
- Organic & Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
- Academy of Scientific and Innovative Research (AcSIR)
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29
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Tavakoli M, Taylor JN, Li CB, Komatsuzaki T, Pressé S. Single Molecule Data Analysis: An Introduction. ADVANCES IN CHEMICAL PHYSICS 2017. [DOI: 10.1002/9781119324560.ch4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meysam Tavakoli
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - J. Nicholas Taylor
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Chun-Biu Li
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
- Department of Mathematics; Stockholm University; 106 91 Stockholm Sweden
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Steve Pressé
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Cell and Integrative Physiology; Indiana University School of Medicine; Indianapolis IN 46202 USA
- Department of Physics and School of Molecular Sciences; Arizona State University; Tempe AZ 85287 USA
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30
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Maksimov EG, Mironov KS, Trofimova MS, Nechaeva NL, Todorenko DA, Klementiev KE, Tsoraev GV, Tyutyaev EV, Zorina AA, Feduraev PV, Allakhverdiev SI, Paschenko VZ, Los DA. Membrane fluidity controls redox-regulated cold stress responses in cyanobacteria. PHOTOSYNTHESIS RESEARCH 2017; 133:215-223. [PMID: 28110449 DOI: 10.1007/s11120-017-0337-333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 01/08/2017] [Indexed: 05/19/2023]
Abstract
Membrane fluidity is the important regulator of cellular responses to changing ambient temperature. Bacteria perceive cold by the transmembrane histidine kinases that sense changes in thickness of the cytoplasmic membrane due to its rigidification. In the cyanobacterium Synechocystis, about a half of cold-responsive genes is controlled by the light-dependent transmembrane histidine kinase Hik33, which also partially controls the responses to osmotic, salt, and oxidative stress. This implies the existence of some universal, but yet unknown signal that triggers adaptive gene expression in response to various stressors. Here we selectively probed the components of photosynthetic machinery and functionally characterized the thermodynamics of cyanobacterial photosynthetic membranes with genetically altered fluidity. We show that the rate of oxidation of the quinone pool (PQ), which interacts with both photosynthetic and respiratory electron transport chains, depends on membrane fluidity. Inhibitor-induced stimulation of redox changes in PQ triggers cold-induced gene expression. Thus, the fluidity-dependent changes in the redox state of PQ may universally trigger cellular responses to stressors that affect membrane properties.
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Affiliation(s)
- Eugene G Maksimov
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Kirill S Mironov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
| | - Marina S Trofimova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
| | - Natalya L Nechaeva
- Chemical Enzymology Department, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Daria A Todorenko
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Konstantin E Klementiev
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Georgy V Tsoraev
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Eugene V Tyutyaev
- Department of Biotechnology, Bioengineering and Biochemistry, Faculty Biotechnology and Biology, Ogarev Mordovia State University, Saransk, Republic of Mordovia, Russia, 430032
| | - Anna A Zorina
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
| | - Pavel V Feduraev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
- Chemical-Biological Institute, Immanuel Kant Federal Baltic University, Kaliningrad, Russia, 236041
| | | | - Vladimir Z Paschenko
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Dmitry A Los
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276.
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31
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Maksimov EG, Mironov KS, Trofimova MS, Nechaeva NL, Todorenko DA, Klementiev KE, Tsoraev GV, Tyutyaev EV, Zorina AA, Feduraev PV, Allakhverdiev SI, Paschenko VZ, Los DA. Membrane fluidity controls redox-regulated cold stress responses in cyanobacteria. PHOTOSYNTHESIS RESEARCH 2017; 133:215-223. [PMID: 28110449 DOI: 10.1007/s11120-017-0337-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 01/08/2017] [Indexed: 06/06/2023]
Abstract
Membrane fluidity is the important regulator of cellular responses to changing ambient temperature. Bacteria perceive cold by the transmembrane histidine kinases that sense changes in thickness of the cytoplasmic membrane due to its rigidification. In the cyanobacterium Synechocystis, about a half of cold-responsive genes is controlled by the light-dependent transmembrane histidine kinase Hik33, which also partially controls the responses to osmotic, salt, and oxidative stress. This implies the existence of some universal, but yet unknown signal that triggers adaptive gene expression in response to various stressors. Here we selectively probed the components of photosynthetic machinery and functionally characterized the thermodynamics of cyanobacterial photosynthetic membranes with genetically altered fluidity. We show that the rate of oxidation of the quinone pool (PQ), which interacts with both photosynthetic and respiratory electron transport chains, depends on membrane fluidity. Inhibitor-induced stimulation of redox changes in PQ triggers cold-induced gene expression. Thus, the fluidity-dependent changes in the redox state of PQ may universally trigger cellular responses to stressors that affect membrane properties.
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Affiliation(s)
- Eugene G Maksimov
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Kirill S Mironov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
| | - Marina S Trofimova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
| | - Natalya L Nechaeva
- Chemical Enzymology Department, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Daria A Todorenko
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Konstantin E Klementiev
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Georgy V Tsoraev
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Eugene V Tyutyaev
- Department of Biotechnology, Bioengineering and Biochemistry, Faculty Biotechnology and Biology, Ogarev Mordovia State University, Saransk, Republic of Mordovia, Russia, 430032
| | - Anna A Zorina
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
| | - Pavel V Feduraev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276
- Chemical-Biological Institute, Immanuel Kant Federal Baltic University, Kaliningrad, Russia, 236041
| | | | - Vladimir Z Paschenko
- Department of Biophysics, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119992
| | - Dmitry A Los
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia, 127276.
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32
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Direct single-molecule measurements of phycocyanobilin photophysics in monomeric C-phycocyanin. Proc Natl Acad Sci U S A 2017; 114:9779-9784. [PMID: 28847963 DOI: 10.1073/pnas.1705435114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phycobilisomes are highly organized pigment-protein antenna complexes found in the photosynthetic apparatus of cyanobacteria and rhodophyta that harvest solar energy and transport it to the reaction center. A detailed bottom-up model of pigment organization and energy transfer in phycobilisomes is essential to understanding photosynthesis in these organisms and informing rational design of artificial light-harvesting systems. In particular, heterogeneous photophysical behaviors of these proteins, which cannot be predicted de novo, may play an essential role in rapid light adaptation and photoprotection. Furthermore, the delicate architecture of these pigment-protein scaffolds sensitizes them to external perturbations, for example, surface attachment, which can be avoided by study in free solution or in vivo. Here, we present single-molecule characterization of C-phycocyanin (C-PC), a three-pigment biliprotein that self-assembles to form the midantenna rods of cyanobacterial phycobilisomes. Using the Anti-Brownian Electrokinetic (ABEL) trap to counteract Brownian motion of single particles in real time, we directly monitor the changing photophysical states of individual C-PC monomers from Spirulina platensis in free solution by simultaneous readout of their brightness, fluorescence anisotropy, fluorescence lifetime, and emission spectra. These include single-chromophore emission states for each of the three covalently bound phycocyanobilins, providing direct measurements of the spectra and photophysics of these chemically identical molecules in their native protein environment. We further show that a simple Förster resonant energy transfer (FRET) network model accurately predicts the observed photophysical states of C-PC and suggests highly variable quenching behavior of one of the chromophores, which should inform future studies of higher-order complexes.
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Abstract
The change point detection method ( Watkins , L. P. ; Yang , H. J. Phys. Chem. B 2005 , 109 , 617 ) allows the objective identification and isolation of abrupt changes along a data series. Because this method is grounded in statistical tests, it is particularly powerful for probing complex and noisy signals without artificially imposing a kinetics model. The original algorithm, however, has a time complexity of [Formula: see text], where N is the size of the data and is, therefore, limited in its scalability. This paper puts forth a parallelization of change point detection to address these time and memory constraints. This parallelization method was evaluated by applying it to changes in the mean of Gaussian-distributed data and found that time decreases superlinearly with respect to the number of processes (i.e., parallelization with two processes takes less than half of the time of one process). Moreover, there was minimal reduction in detection power. These results suggest that our parallelization algorithm is a viable scheme that can be implemented for other change point detection methods.
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Affiliation(s)
- Nancy Song
- Department of Chemistry, Princeton University, , Princeton, New Jersey 08544, United States
| | - Haw Yang
- Department of Chemistry, Princeton University, , Princeton, New Jersey 08544, United States
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34
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Gavrilov M, Bechhoefer J. Feedback traps for virtual potentials. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0217. [PMID: 28115614 PMCID: PMC5311437 DOI: 10.1098/rsta.2016.0217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/15/2016] [Indexed: 06/01/2023]
Abstract
Feedback traps are tools for trapping and manipulating single charged objects, such as molecules in solution. An alternative to optical tweezers and other single-molecule techniques, they use feedback to counteract the Brownian motion of a molecule of interest. The trap first acquires information about a molecule's position and then applies an electric feedback force to move the molecule. Since electric forces are stronger than optical forces at small scales, feedback traps are the best way to trap single molecules without 'touching' them (e.g. by putting them in a small box or attaching them to a tether). Feedback traps can do more than trap molecules: they can also subject a target object to forces that are calculated to be the gradient of a desired potential function U(x). If the feedback loop is fast enough, it creates a virtual potential whose dynamics will be very close to those of a particle in an actual potential U(x). But because the dynamics are entirely a result of the feedback loop-absent the feedback, there is only an object diffusing in a fluid-we are free to specify and then manipulate in time an arbitrary potential U(x,t). Here, we review recent applications of feedback traps to studies on the fundamental connections between information and thermodynamics, a topic where feedback plays an even more fundamental role. We discuss how recursive maximum-likelihood techniques allow continuous calibration, to compensate for drifts in experiments that last for days. We consider ways to estimate work and heat, using them to measure fluctuating energies to a precision of ±0.03 kT over these long experiments. Finally, we compare work and heat measurements of the costs of information erasure, the Landauer limit of kT ln 2 per bit of information erased. We argue that, when you want to know the average heat transferred to a bath in a long protocol, you should measure instead the average work and then infer the heat using the first law of thermodynamics.This article is part of the themed issue 'Horizons of cybernetical physics'.
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Affiliation(s)
- Momčilo Gavrilov
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - John Bechhoefer
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
- Kavli Institute for Theoretical Physics China CAS, Beijing 100190, People's Republic of China
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35
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Kondo T, Chen WJ, Schlau-Cohen GS. Single-Molecule Fluorescence Spectroscopy of Photosynthetic Systems. Chem Rev 2017; 117:860-898. [DOI: 10.1021/acs.chemrev.6b00195] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Toru Kondo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Wei Jia Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Gabriela S. Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
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36
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Gavrilov M, Bechhoefer J. Erasure without Work in an Asymmetric Double-Well Potential. PHYSICAL REVIEW LETTERS 2016; 117:200601. [PMID: 27886493 DOI: 10.1103/physrevlett.117.200601] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 05/25/2023]
Abstract
According to Landauer's principle, erasing a memory requires an average work of at least kTln2 per bit. Recent experiments have confirmed this prediction for a one-bit memory represented by a symmetric double-well potential. Here, we present an experimental study of erasure for a memory encoded in an asymmetric double-well potential. Using a feedback trap, we find that the average work to erase can be less than kTln2. Surprisingly, erasure protocols that differ subtly give measurably different values for the asymptotic work, a result we explain by showing that one protocol is symmetric with the respect to time reversal, while the other is not. The differences between the protocols help clarify the distinctions between thermodynamic and logical reversibility.
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Affiliation(s)
- Momčilo Gavrilov
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - John Bechhoefer
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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37
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Muller EA, Pollard B, Bechtel HA, van Blerkom P, Raschke MB. Infrared vibrational nanocrystallography and nanoimaging. SCIENCE ADVANCES 2016; 2:e1601006. [PMID: 27730212 PMCID: PMC5055384 DOI: 10.1126/sciadv.1601006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/18/2016] [Indexed: 05/24/2023]
Abstract
Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids.
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Affiliation(s)
- Eric A. Muller
- Department of Physics, Department of Chemistry, and JILA, University of Colorado, Boulder, CO 80309, USA
| | - Benjamin Pollard
- Department of Physics, Department of Chemistry, and JILA, University of Colorado, Boulder, CO 80309, USA
| | - Hans A. Bechtel
- Advanced Light Source Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter van Blerkom
- Department of Physics, Department of Chemistry, and JILA, University of Colorado, Boulder, CO 80309, USA
| | - Markus B. Raschke
- Department of Physics, Department of Chemistry, and JILA, University of Colorado, Boulder, CO 80309, USA
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38
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Gwizdala M, Berera R, Kirilovsky D, van Grondelle R, Krüger TP. Controlling Light Harvesting with Light. J Am Chem Soc 2016; 138:11616-22. [DOI: 10.1021/jacs.6b04811] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michal Gwizdala
- Department
of Physics and Astronomy, VU Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Rudi Berera
- Department
of Food Sciences, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Diana Kirilovsky
- Centre National de la Recherche Scientifique (CNRS), I2BC, UMR 9198, 91191 Gif-sur-Yvette, France
- Commissariat
à l’Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif-sur-Yvette, France
| | - Rienk van Grondelle
- Department
of Physics and Astronomy, VU Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department
of Physics, University of Pretoria, 0028 Hatfield, South Africa
| | - Tjaart P.J. Krüger
- Department
of Physics, University of Pretoria, 0028 Hatfield, South Africa
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39
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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40
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Park KD, Muller EA, Kravtsov V, Sass PM, Dreyer J, Atkin JM, Raschke MB. Variable-Temperature Tip-Enhanced Raman Spectroscopy of Single-Molecule Fluctuations and Dynamics. NANO LETTERS 2016; 16:479-87. [PMID: 26679007 DOI: 10.1021/acs.nanolett.5b04135] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Structure, dynamics, and coupling involving single-molecules determine function in catalytic, electronic or biological systems. While vibrational spectroscopy provides insight into molecular structure, rapid fluctuations blur the molecular trajectory even in single-molecule spectroscopy, analogous to spatial averaging in measuring large ensembles. To gain insight into intramolecular coupling, substrate coupling, and dynamic processes, we use tip-enhanced Raman spectroscopy (TERS) at variable and cryogenic temperatures, to slow and control the motion of a single molecule. We resolve intrinsic line widths of individual normal modes, allowing detailed and quantitative investigation of the vibrational modes. From temperature dependent line narrowing and splitting, we quantify ultrafast vibrational dephasing, intramolecular coupling, and conformational heterogeneity. Through statistical correlation analysis of fluctuations of individual modes, we observe rotational motion and spectral fluctuations of the molecule. This work demonstrates single-molecule vibrational spectroscopy beyond chemical identification, opening the possibility for a complete picture of molecular motion ranging from femtoseconds to minutes.
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Affiliation(s)
- Kyoung-Duck Park
- Department of Physics, Department of Chemistry, and JILA, University of Colorado , Boulder, Colorado 80309, United States
| | - Eric A Muller
- Department of Physics, Department of Chemistry, and JILA, University of Colorado , Boulder, Colorado 80309, United States
| | - Vasily Kravtsov
- Department of Physics, Department of Chemistry, and JILA, University of Colorado , Boulder, Colorado 80309, United States
| | - Paul M Sass
- Department of Physics, Department of Chemistry, and JILA, University of Colorado , Boulder, Colorado 80309, United States
| | - Jens Dreyer
- German Research School for Simulation Sciences, RWTH Aachen University and Forschungszentrum Jülich , D-52425 Jülich, Germany
| | - Joanna M Atkin
- Department of Physics, Department of Chemistry, and JILA, University of Colorado , Boulder, Colorado 80309, United States
- Department of Chemistry, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Markus B Raschke
- Department of Physics, Department of Chemistry, and JILA, University of Colorado , Boulder, Colorado 80309, United States
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41
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Abstract
As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many talented scientists all over the world have extended our knowledge of the nanoscale and many microscopic mechanisms previously hidden by ensemble averaging.
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Affiliation(s)
- W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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42
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Dissecting pigment architecture of individual photosynthetic antenna complexes in solution. Proc Natl Acad Sci U S A 2015; 112:13880-5. [PMID: 26438850 DOI: 10.1073/pnas.1514027112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oligomerization plays a critical role in shaping the light-harvesting properties of many photosynthetic pigment-protein complexes, but a detailed understanding of this process at the level of individual pigments is still lacking. To study the effects of oligomerization, we designed a single-molecule approach to probe the photophysical properties of individual pigment sites as a function of protein assembly state. Our method, based on the principles of anti-Brownian electrokinetic trapping of single fluorescent proteins, step-wise photobleaching, and multiparameter spectroscopy, allows pigment-specific spectroscopic information on single multipigment antennae to be recorded in a nonperturbative aqueous environment with unprecedented detail. We focus on the monomer-to-trimer transformation of allophycocyanin (APC), an important antenna protein in cyanobacteria. Our data reveal that the two chemically identical pigments in APC have different roles. One (α) is the functional pigment that red-shifts its spectral properties upon trimer formation, whereas the other (β) is a "protective" pigment that persistently quenches the excited state of α in the prefunctional, monomer state of the protein. These results show how subtleties in pigment organization give rise to functionally important aspects of energy transfer and photoprotection in antenna complexes. The method developed here should find immediate application in understanding the emergent properties of other natural and artificial light-harvesting systems.
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Kim JY, Kim C, Lee NK. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering. Nat Commun 2015; 6:6992. [PMID: 25908552 PMCID: PMC4421855 DOI: 10.1038/ncomms7992] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 03/23/2015] [Indexed: 01/15/2023] Open
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s–1 between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution. Single-molecule fluorescence resonance energy transfer is widely used to probe biomolecular dynamics, but is limited by its temporal resolution. Here, Kim et al. push the limit to submillisecond for the duration of tens of milliseconds by tethering target molecules to liposomes in buffer solutions.
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Affiliation(s)
- Jae-Yeol Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Cheolhee Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Nam Ki Lee
- 1] Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Korea [2] School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, Korea
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44
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Schlau-Cohen GS, Yang HY, Krüger TPJ, Xu P, Gwizdala M, van Grondelle R, Croce R, Moerner WE. Single-Molecule Identification of Quenched and Unquenched States of LHCII. J Phys Chem Lett 2015; 6:860-7. [PMID: 26262664 DOI: 10.1021/acs.jpclett.5b00034] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In photosynthetic light harvesting, absorbed sunlight is converted to electron flow with near-unity quantum efficiency under low light conditions. Under high light conditions, plants avoid damage to their molecular machinery by activating a set of photoprotective mechanisms to harmlessly dissipate excess energy as heat. To investigate these mechanisms, we study the primary antenna complex in green plants, light-harvesting complex II (LHCII), at the single-complex level. We use a single-molecule technique, the Anti-Brownian Electrokinetic trap, which enables simultaneous measurements of fluorescence intensity, lifetime, and spectra in solution. With this approach, including the first measurements of fluorescence lifetime on single LHCII complexes, we access the intrinsic conformational dynamics. In addition to an unquenched state, we identify two partially quenched states of LHCII. Our results suggest that there are at least two distinct quenching sites with different molecular compositions, meaning multiple dissipative pathways in LHCII. Furthermore, one of the quenched conformations significantly increases in relative population under environmental conditions mimicking high light.
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Affiliation(s)
| | - Hsiang-Yu Yang
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tjaart P J Krüger
- ‡Department of Physics, University of Pretoria, Private bag X20, Hatfield 0028, South Africa
| | - Pengqi Xu
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Michal Gwizdala
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Rienk van Grondelle
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Roberta Croce
- §Department of Physics and Astronomy, Faculty of Sciences, VU University Amsterdam and LaserLab Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - W E Moerner
- †Department of Chemistry, Stanford University, Stanford, California 94305, United States
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45
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Filez M, Redekop EA, Poelman H, Galvita VV, Marin GB. Advanced Elemental Characterization during Pt–In Catalyst Formation by Wavelet Transformed X-ray Absorption Spectroscopy. Anal Chem 2015; 87:3520-6. [DOI: 10.1021/acs.analchem.5b00109] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Matthias Filez
- Laboratory for Chemical Technology, Ghent University, Technologiepark 914, B-9052 Ghent, Belgium
| | - Evgeniy A. Redekop
- Laboratory for Chemical Technology, Ghent University, Technologiepark 914, B-9052 Ghent, Belgium
| | - Hilde Poelman
- Laboratory for Chemical Technology, Ghent University, Technologiepark 914, B-9052 Ghent, Belgium
| | - Vladimir V. Galvita
- Laboratory for Chemical Technology, Ghent University, Technologiepark 914, B-9052 Ghent, Belgium
| | - Guy B. Marin
- Laboratory for Chemical Technology, Ghent University, Technologiepark 914, B-9052 Ghent, Belgium
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46
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Abstract
We review studies that quantify newly discovered forces from single enzymatic reactions. These forces arise from the conversion of chemical energy to kinetic energy, which can be harnessed to direct diffusion of the enzyme up a concentration gradient of substrate, a novel phenomenon of molecular chemotaxis. When immobilized, enzymes can move fluid around them and perform directional pumping in microfluidic chambers. Because of the extensive array of enzymes in biological cells, we also develop three new hypotheses: that enzymatic self diffusion can assist in organizing signaling pathways in cells, can assist in pumping of fluid in cells, and can impose biologically significant forces on organelles, which will be manifested as stochastic motion not explained by thermal forces or myosin II. Such mechanochemical phenomena open up new directions in research in mechanobiology in which all enzymes, in addition to their primary function as catalysts for reactions, may have secondary functions as initiators of mechanosensitive transduction pathways.
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Affiliation(s)
- Peter J Butler
- Department of Biomedical Engineering, The Pennsylvania State University, 205 Hallowell Building, University Park, PA 16802, USA
| | - Krishna K Dey
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA
| | - Ayusman Sen
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA
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47
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Long S, Zhou M, Tang K, Zeng XL, Niu Y, Guo Q, Zhao KH, Xia A. Single-molecule spectroscopy and femtosecond transient absorption studies on the excitation energy transfer process in ApcE(1–240) dimers. Phys Chem Chem Phys 2015; 17:13387-96. [DOI: 10.1039/c5cp01687h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The red-shifted absorption of ApcE dimers results from extending chromophore conformation, which does not depend on strong exction coupling.
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Affiliation(s)
- Saran Long
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Meng Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Kun Tang
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- People's Republic of China
| | - Xiao-Li Zeng
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- People's Republic of China
| | - Yingli Niu
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Qianjin Guo
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- People's Republic of China
| | - Andong Xia
- Beijing National Laboratory for Molecular Sciences (BNLMS) and Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
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48
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Stopel MHW, Blum C, Subramaniam V. Excitation Spectra and Stokes Shift Measurements of Single Organic Dyes at Room Temperature. J Phys Chem Lett 2014; 5:3259-3264. [PMID: 26276342 DOI: 10.1021/jz501536a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report measurements of excitation and emission spectra of single, polymer-embedded, perylene dye molecules at room temperature. From these measurements, we can derive the Stokes shift for each single molecule. We determined the distribution of excitation and emission peak energies and, thus, the distribution of single molecule Stokes shifts. Single molecule Stokes shifts have not been recorded to date, and the Stokes shift has often been assumed to be constant in single molecule studies. Our data show that the observed spectral heterogeneity in single molecule emission originates not only from synchronous energetic shifts of the excitation and the emission spectra but also from variations in the Stokes shift, speaking against the assumption of constant Stokes shift.
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Affiliation(s)
- Martijn H W Stopel
- †Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Christian Blum
- †Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- †Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- ‡Nanobiophysics, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- §FOM Institute AMOLF, 104 Science Park, 1098 XG Amsterdam, The Netherlands
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49
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Kayci M, Chang HC, Radenovic A. Electron spin resonance of nitrogen-vacancy defects embedded in single nanodiamonds in an ABEL trap. NANO LETTERS 2014; 14:5335-41. [PMID: 25111386 DOI: 10.1021/nl5023964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Room temperature optically detected magnetic resonance of a single quantum object with nanoscale position control is an outstanding challenge in many areas, particularly in the life sciences. We introduce a novel approach to control the nitrogen-vacancy (NV) centers hosted in a single fluorescent nanodiamond (FND) for which an anti-Brownian electrokinetic trap (ABEL) performs the position control and an integrated radiofrequency (RF) circuit provides enhanced magnetic flux density for ensemble spin-state control simultaneously. We demonstrate static magnetic field sensing in platforms compatible with ABEL trap. With the advances in the synthesis and functionalization of stable arbitrarily small FNDs, we foresee the use of our device for the trapping and manipulation of single molecular-sized FNDs in aqueous solution.
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Affiliation(s)
- Metin Kayci
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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50
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Gavrilov M, Jun Y, Bechhoefer J. Real-time calibration of a feedback trap. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:095102. [PMID: 25273767 DOI: 10.1063/1.4894383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Feedback traps use closed-loop control to trap or manipulate small particles and molecules in solution. They have been applied to the measurement of physical and chemical properties of particles and to explore fundamental questions in the non-equilibrium statistical mechanics of small systems. These applications have been hampered by drifts in the electric forces used to manipulate the particles. Although the drifts are small for measurements on the order of seconds, they dominate on time scales of minutes or slower. Here, we show that a recursive maximum likelihood (RML) algorithm can allow real-time measurement and control of electric and stochastic forces over time scales of hours. Simulations show that the RML algorithm recovers known parameters accurately. Experimental estimates of diffusion coefficients are also consistent with expected physical properties.
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Affiliation(s)
- Momčilo Gavrilov
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yonggun Jun
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - John Bechhoefer
- Department of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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