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Li Y, Yu X, Qu T, Ng J, Lin Z, Zhang L, Chen J. Optomechanical effects caused by non-zero field quantities in multiple evanescent waves. OPTICS EXPRESS 2023; 31:44004-44018. [PMID: 38178482 DOI: 10.1364/oe.506758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/16/2023] [Indexed: 01/06/2024]
Abstract
Evanescent waves, with their high energy density, intricate local momentum, and spatial distribution of spins, have been the subject of extensive recent study. These waves offer promising applications in near-field particle manipulation. Consequently, it becomes imperative to gain a deeper understanding of the impacts of scattering and gradient forces on particles in evanescent waves to enhance and refine the manipulation capabilities. In this study, we employ the multipole expansion theory to present analytical expressions for the scattering and gradient forces exerted on an isotropic sphere of any size and composition in multiple evanescent waves. The investigation of these forces reveals several unusual optomechanical phenomena. It is well known that the scattering force does not exist in counter-propagating homogeneous plane waves. Surprisingly, in multiple pairs of counter-propagating evanescent waves, the scattering force can arise due to the nonzero orbital momentum (OM) density and/or the curl part of the imaginary Poynting momentum (IPM) density. More importantly, it is found that the optical scattering force can be switched on and off by simply tuning the polarization. Furthermore, optical forces typically vary with spatial position in an interference field. However, in the interference field generated by evanescent waves, the gradient force becomes a spatial constant in the propagating plane as the particle's radius increases. This is attributed to the decisive role of the non-interference term of the electromagnetic energy density gradient. Our study establishes a comprehensive and rigorous theoretical foundation, propelling the advancement and optimization of optical manipulation techniques harnessed through multiple evanescent waves. Specifically, these insights hold promise in elevating trapping efficiency through precise control and manipulation of optical scattering and gradient forces, stimulating further explorations.
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2
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Nguyen TD, Chen YI, Chen LH, Yeh HC. Recent Advances in Single-Molecule Tracking and Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:253-284. [PMID: 37314878 DOI: 10.1146/annurev-anchem-091922-073057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.
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Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Limin H Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Texas Materials Institute, University of Texas at Austin, Austin, Texas, USA
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3
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Tripathy SP, Ponnapati M, Bhat S, Jacobson J, Chatterjee P. Femtomolar detection of SARS-CoV-2 via peptide beacons integrated on a miniaturized TIRF microscope. SCIENCE ADVANCES 2022; 8:eabn2378. [PMID: 36001655 PMCID: PMC9401610 DOI: 10.1126/sciadv.abn2378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/13/2022] [Indexed: 05/29/2023]
Abstract
The novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to pose a substantial global health threat. Along with vaccines and targeted therapeutics, there is a critical need for rapid diagnostic solutions. In this work, we use computational protein modeling tools to suggest molecular beacon architectures that function as conformational switches for high-sensitivity detection of the SARS-CoV-2 spike protein receptor binding domain (S-RBD). Integrating these beacons on a miniaturized total internal reflection fluorescence (mini-TIRF) microscope, we detect the S-RBD and pseudotyped SARS-CoV-2 with limits of detection in the femtomolar range. We envision that our designed mini-TIRF platform will serve as a robust platform for point-of-care diagnostics for SARS-CoV-2 and future emergent viral threats.
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Affiliation(s)
- Soumya P. Tripathy
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manvitha Ponnapati
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Suhaas Bhat
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Joseph Jacobson
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pranam Chatterjee
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, USA
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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4
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Ghimire ML, Gibbs DR, Mahmoud R, Dhakal S, Reiner JE. Nanopore Analysis as a Tool for Studying Rapid Holliday Junction Dynamics and Analyte Binding. Anal Chem 2022; 94:10027-10034. [PMID: 35786863 DOI: 10.1021/acs.analchem.2c00342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Holliday junctions (HJs) are an important class of nucleic acid structure utilized in DNA break repair processes. As such, these structures have great importance as therapeutic targets and for understanding the onset and development of various diseases. Single-molecule fluorescence resonance energy transfer (smFRET) has been used to study HJ structure-fluctuation kinetics, but given the rapid time scales associated with these kinetics (approximately sub-milliseconds) and the limited bandwidth of smFRET, these studies typically require one to slow down the structure fluctuations using divalent ions (e.g., Mg2+). This modification limits the ability to understand and model the underlying kinetics associated with HJ fluctuations. We address this here by utilizing nanopore sensing in a gating configuration to monitor DNA structure fluctuations without divalent ions. A nanopore analysis shows that HJ fluctuations occur on the order of 0.1-10 ms and that the HJ remains locked in a single conformation with short-lived transitions to a second conformation. It is not clear what role the nanopore plays in affecting these kinetics, but the time scales observed indicate that HJs are capable of undergoing rapid transitions that are not detectable with lower bandwidth measurement techniques. In addition to monitoring rapid HJ fluctuations, we also report on the use of nanopore sensing to develop a highly selective sensor capable of clear and rapid detection of short oligo DNA strands that bind to various HJ targets.
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Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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5
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Abstract
The precise assembly and disassembly of actin filaments is required for several cellular processes, and their regulation has been scrutinized for decades. Twenty years ago, a handful of studies marked the advent of a new type of experiment to study actin dynamics: using optical microscopy to look at individual events, taking place on individual filaments in real time. Here, we summarize the main characteristics of this approach and how it has changed our ability to understand actin assembly dynamics. We also highlight some of its caveats and reflect on what we have learned over the past 20 years, leading us to propose a set of guidelines, which we hope will contribute to a better exploitation of this powerful tool.
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6
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Małecka EM, Hua B, Woodson SA. Single-Molecule FRET Studies of RNA Structural Rearrangements and RNA-RNA Interactions. Methods Mol Biol 2022; 2518:271-289. [PMID: 35666451 PMCID: PMC10052914 DOI: 10.1007/978-1-0716-2421-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA-guided regulation of gene expression is found in all cell types. In this mode of regulation, antisense interactions between the regulatory RNA and its target are typically facilitated by a protein partner. Single-molecule fluorescence microscopy is a powerful tool for dissecting the conformational states and intermediates that contribute to target recognition. This chapter describes protocols for studying target recognition by bacterial small RNAs and their chaperone Hfq on the single-molecule level, using a total internal reflection fluorescence microscope. The sections cover the design of suitable RNA substrates for sRNA-mRNA annealing reactions, preparation of internally labeled mRNA for detecting conformational changes in the target, and key steps of the data analysis. These protocols can be adapted to other RNA-binding proteins that chaperone RNA interactions.
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Affiliation(s)
- Ewelina M Małecka
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Boyang Hua
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, MD, USA
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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7
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Yoshimura H. Potential of Single-Molecule Live-Cell Imaging for Chemical Translational Biology. Chembiochem 2021; 22:2941-2945. [PMID: 34254418 DOI: 10.1002/cbic.202100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/05/2021] [Indexed: 11/11/2022]
Abstract
Single-molecule live-cell imaging is the most direct approach for monitoring the motility of molecules in living cells. Considering the relationship between the motility of molecules and their function, information obtained from single-molecule imaging involves essential clues for understanding the regulatory mechanisms of the processes of target molecules, and translation to applied sciences such as drug discovery. In this Concept, examples of single-molecule imaging studies on G protein-coupled receptors (GPCRs) are mainly introduced, and recent techniques of single-molecule imaging for overcoming the limitation of single-molecule live-cell imaging are discussed. Based on these studies, the prospects of single-molecule imaging will be outlined.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 1130033, Japan
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8
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Colombo J, Antkowiak A, Kogan K, Kotila T, Elliott J, Guillotin A, Lappalainen P, Michelot A. A functional family of fluorescent nucleotide analogues to investigate actin dynamics and energetics. Nat Commun 2021; 12:548. [PMID: 33483497 PMCID: PMC7822861 DOI: 10.1038/s41467-020-20827-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 12/15/2020] [Indexed: 01/30/2023] Open
Abstract
Actin polymerization provides force for vital processes of the eukaryotic cell, but our understanding of actin dynamics and energetics remains limited due to the lack of high-quality probes. Most current probes affect dynamics of actin or its interactions with actin-binding proteins (ABPs), and cannot track the bound nucleotide. Here, we identify a family of highly sensitive fluorescent nucleotide analogues structurally compatible with actin. We demonstrate that these fluorescent nucleotides bind to actin, maintain functional interactions with a number of essential ABPs, are hydrolyzed within actin filaments, and provide energy to power actin-based processes. These probes also enable monitoring actin assembly and nucleotide exchange with single-molecule microscopy and fluorescence anisotropy kinetics, therefore providing robust and highly versatile tools to study actin dynamics and functions of ABPs.
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Affiliation(s)
- Jessica Colombo
- grid.462081.90000 0004 0598 4854Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, 13288 Marseille, France
| | - Adrien Antkowiak
- grid.462081.90000 0004 0598 4854Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, 13288 Marseille, France
| | - Konstantin Kogan
- grid.7737.40000 0004 0410 2071HiLIFE Institute of Biotechnology, P.O. Box 56, University of Helsinki, 00014 Helsinki, Finland
| | - Tommi Kotila
- grid.7737.40000 0004 0410 2071HiLIFE Institute of Biotechnology, P.O. Box 56, University of Helsinki, 00014 Helsinki, Finland
| | - Jenna Elliott
- grid.462081.90000 0004 0598 4854Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, 13288 Marseille, France
| | - Audrey Guillotin
- grid.462081.90000 0004 0598 4854Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, 13288 Marseille, France
| | - Pekka Lappalainen
- grid.7737.40000 0004 0410 2071HiLIFE Institute of Biotechnology, P.O. Box 56, University of Helsinki, 00014 Helsinki, Finland
| | - Alphée Michelot
- grid.462081.90000 0004 0598 4854Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, 13288 Marseille, France
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9
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Ušaj M, Moretto L, Vemula V, Salhotra A, Månsson A. Single molecule turnover of fluorescent ATP by myosin and actomyosin unveil elusive enzymatic mechanisms. Commun Biol 2021; 4:64. [PMID: 33441912 PMCID: PMC7806905 DOI: 10.1038/s42003-020-01574-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 12/04/2020] [Indexed: 01/10/2023] Open
Abstract
Benefits of single molecule studies of biomolecules include the need for minimal amounts of material and the potential to reveal phenomena hidden in ensembles. However, results from recent single molecule studies of fluorescent ATP turnover by myosin are difficult to reconcile with ensemble studies. We found that key reasons are complexities due to dye photophysics and fluorescent contaminants. After eliminating these, through surface cleaning and use of triple state quenchers and redox agents, the distributions of ATP binding dwell times on myosin are best described by 2 to 3 exponential processes, with and without actin, and with and without the inhibitor para-aminoblebbistatin. Two processes are attributable to ATP turnover by myosin and actomyosin respectively, whereas the remaining process (rate constant 0.2–0.5 s−1) is consistent with non-specific ATP binding to myosin, possibly accelerating ATP transport to the active site. Finally, our study of actin-activated myosin ATP turnover without sliding between actin and myosin reveals heterogeneity in the ATP turnover kinetics consistent with models of isometric contraction. With fluorescence based-TIRF microspectroscopy, Ušaj et al. unveil mechanistic details about the ATP turnover rates by myosin and actomyosin with enzymatic reaction pathways that were not possible to obtain from ensemble studies. This study could be important to the field of molecular motors.
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Affiliation(s)
- Marko Ušaj
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE391 82, Kalmar, Sweden.
| | - Luisa Moretto
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE391 82, Kalmar, Sweden
| | - Venukumar Vemula
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE391 82, Kalmar, Sweden
| | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE391 82, Kalmar, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, SE391 82, Kalmar, Sweden.
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10
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Affiliation(s)
- Jörg Enderlein
- Georg August University, Third Institute of Physics - Biophysics, Göttingen, Germany.
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11
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Gortari AN, Bouchoule S, Cambril E, Cattoni A, Hauke L, Enderlein J, Rehfeldt F, Yacomotti A. Metasurface-based total internal reflection microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:1967-1976. [PMID: 32341860 PMCID: PMC7173909 DOI: 10.1364/boe.385276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/21/2020] [Accepted: 03/06/2020] [Indexed: 06/01/2023]
Abstract
Recent years have seen a tremendous progress in the development of dielectric metasurfaces for visible light applications. Such metasurfaces are ultra-thin optical devices that can manipulate optical wavefronts in an arbitrary manner. Here, we present a newly developed metasurface which allows for coupling light into a microscopy coverslip to achieve total internal reflection (TIR) excitation. TIR fluorescence microscopy (TIRFM) is an important bioimaging technique used specifically to image cellular membranes or surface-localized molecules with high contrast and low background. Its most commonly used modality is objective-type TIRFM where one couples a focused excitation laser beam at the edge of the back focal aperture of an oil-immersion objective with high numerical aperture (N.A.) to realize a high incident-angle plane wave excitation above the critical TIR angle in sample space. However, this requires bulky and expensive objectives with a limited field-of-view (FOV). The metasurface which we describe here represents a low cost and easy-to-use alternative for TIRFM. It consists of periodic 2D arrays of asymmetric structures fabricated in TiO2 on borosilicate glass. It couples up to 70% of the incident non-reflected light into the first diffraction order at an angle of 65° in glass, which is above the critical TIR angle for a glass-water interface. Only ∼7% of the light leaks into propagating modes traversing the glass surface, thus minimizing any spurious background fluorescence originating far outside the glass substrate. We describe in detail design and fabrication of the metasurface, and validate is applicability for TIRFM by imaging immunostained human mesenchymal stem cells over a FOV of 200 µm x 200 µm. We envision that these kinds of metasurfaces can become a valuable tool for low-cost and TIRFM, offering high contrast, low photodamage, and high surface selectivity in fluorescence excitation and detection.
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Affiliation(s)
- Antu Nehuen Gortari
- Ctr. de Nanosciences et de Nanotechnologies, Univ. Paris-Sud, Univ. Paris-Saclay, France
| | - Sophie Bouchoule
- Ctr. de Nanosciences et de Nanotechnologies, Univ. Paris-Sud, Univ. Paris-Saclay, France
| | - Edmond Cambril
- Ctr. de Nanosciences et de Nanotechnologies, Univ. Paris-Sud, Univ. Paris-Saclay, France
| | - Andrea Cattoni
- Ctr. de Nanosciences et de Nanotechnologies, Univ. Paris-Sud, Univ. Paris-Saclay, France
| | - Lara Hauke
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
| | - Florian Rehfeldt
- Third Institute of Physics-Biophysics, Georg August University, Göttingen, Germany
| | - Alejandro Yacomotti
- Ctr. de Nanosciences et de Nanotechnologies, Univ. Paris-Sud, Univ. Paris-Saclay, France
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12
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Liu SL, Wang ZG, Xie HY, Liu AA, Lamb DC, Pang DW. Single-Virus Tracking: From Imaging Methodologies to Virological Applications. Chem Rev 2020; 120:1936-1979. [PMID: 31951121 PMCID: PMC7075663 DOI: 10.1021/acs.chemrev.9b00692] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Uncovering
the mechanisms of virus infection and assembly is crucial
for preventing the spread of viruses and treating viral disease. The
technique of single-virus tracking (SVT), also known as single-virus
tracing, allows one to follow individual viruses at different parts
of their life cycle and thereby provides dynamic insights into fundamental
processes of viruses occurring in live cells. SVT is typically based
on fluorescence imaging and reveals insights into previously unreported
infection mechanisms. In this review article, we provide the readers
a broad overview of the SVT technique. We first summarize recent advances
in SVT, from the choice of fluorescent labels and labeling strategies
to imaging implementation and analytical methodologies. We then describe
representative applications in detail to elucidate how SVT serves
as a valuable tool in virological research. Finally, we present our
perspectives regarding the future possibilities and challenges of
SVT.
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Affiliation(s)
- Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Hai-Yan Xie
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , P. R. China
| | - An-An Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), and Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM) , Ludwig-Maximilians-Universität , München , 81377 , Germany
| | - Dai-Wen Pang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine , Nankai University , Tianjin 300071 , P. R. China.,College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, The Institute for Advanced Studies, and Wuhan Institute of Biotechnology , Wuhan University , Wuhan 430072 , P. R. China
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13
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Matsuda K, Sugawa M, Yamagishi M, Kodera N, Yajima J. Visualizing dynamic actin cross‐linking processes driven by the actin‐binding protein anillin. FEBS Lett 2019; 594:1237-1247. [DOI: 10.1002/1873-3468.13720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Kyohei Matsuda
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
| | - Mitsuhiro Sugawa
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
- Komaba Institute for Science The University of Tokyo Japan
| | - Masahiko Yamagishi
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
- Komaba Institute for Science The University of Tokyo Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI‐NanoLSI) Kanazawa University Japan
| | - Junichiro Yajima
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Japan
- Komaba Institute for Science The University of Tokyo Japan
- Research Center for Complex Systems Biology The University of Tokyo Japan
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14
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Yokota H. Fluorescence microscopy for visualizing single-molecule protein dynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129362. [PMID: 31078674 DOI: 10.1016/j.bbagen.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/26/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
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15
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Abstract
This chapter describes methods for high-speed, unloaded, in vitro single-molecule kinesin tracking experiments. Instructions are presented for constructing a total internal reflection dark-field microscope (TIRDFM) and labeling motors with gold nanoparticles. An AMP-PNP unlocking assay is introduced as a specialized means of capturing processive events in a reduced field of view. Finally, step-finding tools for analyzing high frame-rate tracking data are described.
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16
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Lim WM, Ito Y, Sakata-Sogawa K, Tokunaga M. CLIP-170 is essential for MTOC repositioning during T cell activation by regulating dynein localisation on the cell surface. Sci Rep 2018; 8:17447. [PMID: 30487641 PMCID: PMC6261991 DOI: 10.1038/s41598-018-35593-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/06/2018] [Indexed: 02/02/2023] Open
Abstract
The microtubule-organizing centre (MTOC) is repositioned to the centre of the contacted cell surface, the immunological synapse, during T cell activation. However, our understanding of its molecular mechanism remains limited. Here, we found that the microtubule plus-end tracking cytoplasmic linker protein 170 (CLIP-170) plays a novel role in MTOC repositioning using fluorescence imaging. Inhibition of CLIP-170 phosphorylation impaired both MTOC repositioning and interleukin-2 (IL-2) expression. T cell stimulation induced some fraction of dynein to colocalise with CLIP-170 and undergo plus-end tracking. Concurrently, it increased dynein in minus-end-directed movement. It also increased dynein relocation to the centre of the contact surface. Dynein not colocalised with CLIP-170 showed both an immobile state and minus-end-directed movement at a velocity in good agreement with the velocity of MTOC repositioning, which suggests that dynein at the immunological synapse may pull the microtubules and the MTOC. Although CLIP-170 is phosphorylated by AMP-activated protein kinase (AMPK) irrespective of stimulation, phosphorylated CLIP-170 is essential for dynein recruitment to plus-end tracking and for dynein relocation. This indicates that dynein relocation results from coexistence of plus-end- and minus-end-directed translocation. In conclusion, CLIP-170 plays an indispensable role in MTOC repositioning and full activation of T cells by regulating dynein localisation.
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Affiliation(s)
- Wei Ming Lim
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Kumiko Sakata-Sogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan.
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, Kanagawa, 226-8501, Japan.
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Yasui M, Hiroshima M, Kozuka J, Sako Y, Ueda M. Automated single-molecule imaging in living cells. Nat Commun 2018; 9:3061. [PMID: 30076305 PMCID: PMC6076334 DOI: 10.1038/s41467-018-05524-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 07/11/2018] [Indexed: 01/26/2023] Open
Abstract
An automated single-molecule imaging system developed for live-cell analyses based on artificial intelligence-assisted microscopy is presented. All significant procedures, i.e., searching for cells suitable for observation, detecting in-focus positions, and performing image acquisition and single-molecule tracking, are fully automated, and numerous highly accurate, efficient, and reproducible single-molecule imaging experiments in living cells can be performed. Here, the apparatus is applied for single-molecule imaging and analysis of epidermal growth factor receptors (EGFRs) in 1600 cells in a 96-well plate within 1 day. Changes in the lateral mobility of EGFRs on the plasma membrane in response to various ligands and drug concentrations are clearly detected in individual cells, and several dynamic and pharmacological parameters are determined, including the diffusion coefficient, oligomer size, and half-maximal effective concentration (EC50). Automated single-molecule imaging for systematic cell signaling analyses is feasible and can be applied to single-molecule screening, thus extensively contributing to biological and pharmacological research.
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Affiliation(s)
- Masato Yasui
- Laboratory for Cell Signaling Dynamics, RIKEN BDR, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Michio Hiroshima
- Laboratory for Cell Signaling Dynamics, RIKEN BDR, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-198, Japan
| | - Jun Kozuka
- Laboratory for Cell Signaling Dynamics, RIKEN BDR, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-198, Japan.
| | - Masahiro Ueda
- Laboratory for Cell Signaling Dynamics, RIKEN BDR, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan.
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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18
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Crouch GM, Han D, Bohn PW. Zero-Mode Waveguide Nanophotonic Structures for Single Molecule Characterization. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:193001. [PMID: 34158676 PMCID: PMC8216246 DOI: 10.1088/1361-6463/aab8be] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (μM - mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer (smFRET), and fluorescence correlation spectroscopy (FCS) for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs (E-ZMW). In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.
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Affiliation(s)
- Garrison M. Crouch
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Donghoon Han
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
- Departmemt of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
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19
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Lee D, Hwang J, Seo Y, Gilad AA, Choi J. Optical Immunosensors for the Efficient Detection of Target Biomolecules. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0087-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Abstract
Transmembrane protein 16F (TMEM16F) is a Ca2+-dependent phospholipid scramblase that translocates phospholipids bidirectionally between the leaflets of the plasma membrane. Phospholipid scrambling of TMEM16F causes exposure of phosphatidylserine in activated platelets to induce blood clotting and in differentiated osteoblasts to promote bone mineralization. Despite the importance of TMEM16F-mediated phospholipid scrambling in various biological reactions, the fundamental features of the scrambling reaction remain elusive due to technical difficulties in the preparation of a platform for assaying scramblase activity in vitro. Here, we established a method to express and purify mouse TMEM16F as a dimeric molecule by constructing a stable cell line and developed a microarray containing membrane bilayers with asymmetrically distributed phospholipids as a platform for single-molecule scramblase assays. The purified TMEM16F was integrated into the microarray, and monitoring of phospholipid translocation showed that a single TMEM16F molecule transported phospholipids nonspecifically between the membrane bilayers in a Ca2+-dependent manner. Thermodynamic analysis of the reaction indicated that TMEM16F transported 4.5 × 104 lipids per second at 25 °C, with an activation free energy of 47 kJ/mol. These biophysical features were similar to those observed with channels, which transport substrates by facilitating diffusion, and supported the stepping-stone model for the TMEM16F phospholipid scramblase.
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21
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Yazawa K, Furusawa H. Probing Multiple Binding Modes of DNA Hybridization: A Comparison between Single-Molecule Observations and Ensemble Measurements. ACS OMEGA 2018; 3:2084-2092. [PMID: 30023822 PMCID: PMC6045368 DOI: 10.1021/acsomega.8b00135] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/09/2018] [Indexed: 05/04/2023]
Abstract
Interactions between biomolecules are generally analyzed by ensemble measurements, assuming that the interactions occur in a single binding manner. However, such interactions may occur via multiple binding modes. We investigated the kinetics of DNA hybridization as a multiple dynamic model of biomolecular interactions. Two kinetic analyses were performed with a single-molecule observation using total internal reflection fluorescence microscopy (TIRFM) and with ensemble measurements using a quartz-crystal microbalance (QCM) biosensor. We observed the DNA hybridization of 8 and 12 bp DNAs with random sequences and dA12-dT12 and calculated the kinetic parameters, including the dissociation rate constant (koff). Hybridization of 8 bp DNA proceeded mainly via a single binding mode. However, hybridization of 12 bp DNA indicated at least two different binding modes and dA12-dT12 hybridization showed multiple binding modes. For the multiple binding interactions, the kinetic parameters obtained from TIRFM and QCM were different because kinetic parameters obtained from QCM indicate average number of molecules, whereas those from TIRFM indicate average association time. The present study revealed the details of multiple interactions, which can be utilized for better understanding of not only DNA hybridization but also biomolecular interaction mechanisms.
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Affiliation(s)
- Kenjiro Yazawa
- Graduate
School of Science and Engineering and Innovative Flex Course for Frontier
Organic Material Systems (iFront), Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Hiroyuki Furusawa
- Graduate
School of Science and Engineering and Innovative Flex Course for Frontier
Organic Material Systems (iFront), Yamagata
University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
- E-mail: . Phone/Fax: +81-238-26-3841
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22
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Suzuki KGN, Ando H, Komura N, Fujiwara T, Kiso M, Kusumi A. Unraveling of Lipid Raft Organization in Cell Plasma Membranes by Single-Molecule Imaging of Ganglioside Probes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1104:41-58. [DOI: 10.1007/978-981-13-2158-0_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Kuroda C, Ohki Y, Fujimaki M. Optimization of a waveguide-mode sensing chip for an ultraviolet near-field illumination biosensor. OPTICS EXPRESS 2017; 25:26011-26019. [PMID: 29041263 DOI: 10.1364/oe.25.026011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
A waveguide-mode sensor with a planar sensing chip, consisting of two waveguiding layers and a glass substrate, is a promising candidate for a near-field illumination biosensor. Aiming at using fluorescent labeling induced by ultraviolet light, we optimize the structure of a waveguide-mode sensing chip, based on the mechanism for enhancing ultraviolet near-field light revealed by numerical calculations. Candidates of optimal materials are also presented. The chip optimized as above should be able to enhance the intensity of ultraviolet near-field light 25 times as high as an Al surface plasmon resonance sensing chip.
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Multi-color single-molecule tracking and subtrajectory analysis for quantification of spatiotemporal dynamics and kinetics upon T cell activation. Sci Rep 2017; 7:6994. [PMID: 28765585 PMCID: PMC5539329 DOI: 10.1038/s41598-017-06960-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/20/2017] [Indexed: 11/08/2022] Open
Abstract
The dynamic properties of molecules in living cells are attracting increasing interest. We propose a new method, moving subtrajectory analysis using single-molecule tracking, and demonstrate its utility in the spatiotemporal quantification of not only dynamics but also the kinetics of interactions using single-color images. Combining this technique with three-color simultaneous single-molecule imaging, we quantified the dynamics and kinetics of molecules in spatial relation to T cell receptor (TCR) microclusters, which trigger TCR signaling. CD3ε, a component of the TCR/CD3 complex, and CD45, a phosphatase positively and negatively regulating signaling, were each found in two mobility states: faster (associated) and slower (dissociated) states. Dynamics analysis suggests that the microclusters are loosely composed of heterogeneous nanoregions, possibly surrounded by a weak barrier. Kinetics analysis quantified the association and dissociation rates of interactions with the microclusters. The associations of both CD3ε and CD45 were single-step processes. In contrast, their dissociations were each composed of two components, indicating transient and stable associated states. Inside the microclusters, the association was accelerated, and the stable association was increased. Only CD45 showed acceleration of association at the microcluster boundary, suggesting specific affinity on the boundary. Thus, this method is an innovative and versatile tool for spatiotemporal quantification.
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25
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Direct Imaging of Intracellular Signaling Molecule Responsible for the Bacterial Chemotaxis. Methods Mol Biol 2017. [PMID: 28389957 DOI: 10.1007/978-1-4939-6927-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
To elucidate the mechanisms by which cells respond to extracellular stimuli, the behavior of intracellular signaling proteins in a single cell should be directly examined, while simultaneously recording the cellular response. In Escherichia coli, an extracellular chemotactic stimulus is thought to induce a switch in the rotational direction of the flagellar motor, elicited by the binding and dissociation of the phosphorylated form of CheY (CheY-P) to and from the motor. We recently provided direct evidence for the binding of CheY-P to a functioning flagellar motor in live cells. Here, we describe the method for simultaneously measuring the fluorescent signal of the CheY-enhanced green fluorescent protein fusion protein (CheY-EGFP) and the rotational switching of the flagellar motor. By performing fluorescence and bright-field microscopy simultaneously, the rotational switch of the flagellar motor was shown to be induced by the binding and dissociation of CheY-P, and the number of CheY-P molecules bound to the motor was estimated.
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26
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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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27
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YANAGIDA T, ISHII Y. Single molecule detection, thermal fluctuation and life. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:51-63. [PMID: 28190869 PMCID: PMC5422627 DOI: 10.2183/pjab.93.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines.
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Affiliation(s)
- Toshio YANAGIDA
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Center for Information and Neural Network (CiNet), Suita, Osaka, Japan
- Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan
- World Premier International Research Center, Immunology Frontier Research Center, Osaka University, Suita Osaka, Japan
| | - Yoshiharu ISHII
- Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan
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28
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Direct observation of rotation and steps of the archaellum in the swimming halophilic archaeon Halobacterium salinarum. Nat Microbiol 2016; 1:16148. [PMID: 27564999 DOI: 10.1038/nmicrobiol.2016.148] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/18/2016] [Indexed: 11/09/2022]
Abstract
Motile archaea swim using a rotary filament, the archaellum, a surface appendage that resembles bacterial flagella structurally, but is homologous to bacterial type IV pili. Little is known about the mechanism by which archaella produce motility. To gain insights into this mechanism, we characterized archaellar function in the model organism Halobacterium salinarum. Three-dimensional tracking of quantum dots enabled visualization of the left-handed corkscrewing of archaea in detail. An advanced analysis method combined with total internal reflection fluorescence microscopy, termed cross-kymography, was developed and revealed a right-handed helical structure of archaella with a rotation speed of 23 ± 5 Hz. Using these structural and kinetic parameters, we computationally reproduced the swimming and precession motion with a hydrodynamic model and estimated the archaellar motor torque to be 50 pN nm. Finally, in a tethered-cell assay, we observed intermittent pauses during rotation with ∼36° or 60° intervals, which we speculate may be a unitary step consuming a single adenosine triphosphate molecule, which supplies chemical energy of 80 pN nm when hydrolysed. From an estimate of the energy input as ten or six adenosine triphosphates per revolution, the efficiency of the motor is calculated to be ∼6-10%.
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29
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Substrate-dependent dynamics of the multidrug efflux transporter AcrB of Escherichia coli. Sci Rep 2016; 6:21909. [PMID: 26916090 PMCID: PMC4768149 DOI: 10.1038/srep21909] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
The resistance-nodulation-cell division (RND)-type xenobiotic efflux system plays a major role in the multidrug resistance of gram-negative bacteria. The only constitutively expressed RND system of Escherichia coli consists of the inner membrane transporter AcrB, the membrane fusion protein AcrA, and the outer membrane channel TolC. The latter two components are shared with another RND-type transporter AcrD, whose expression is induced by environmental stimuli. Here, we demonstrate how RND-type ternary complexes, which span two membranes and the cell wall, form in vivo. Total internal reflection fluorescence (TIRF) microscopy revealed that most fluorescent foci formed by AcrB fused to green fluorescent protein (GFP) were stationary in the presence of TolC but showed lateral displacements when tolC was deleted. The fraction of stationary AcrB-GFP foci decreased with increasing levels of AcrD. We propose that the AcrB-containing complex becomes unstable upon the induction of AcrD, which presumably replaces AcrB, a process we call “transporter exchange.” This instability is suppressed by AcrB-specific substrates, suggesting that the ternary complex is stabilised when it is in action. These results suggest that the assembly of the RND-type efflux system is dynamically regulated in response to external stimuli, shedding new light on the adaptive antibiotic resistance of bacteria.
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30
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Uchihashi T, Watanabe H, Fukuda S, Shibata M, Ando T. Functional extension of high-speed AFM for wider biological applications. Ultramicroscopy 2016; 160:182-196. [DOI: 10.1016/j.ultramic.2015.10.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 09/25/2015] [Accepted: 10/12/2015] [Indexed: 11/24/2022]
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31
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Yoshimura H, Ozawa T. Monitoring of RNA Dynamics in Living Cells Using PUM-HD and Fluorescent Protein Reconstitution Technique. Methods Enzymol 2016; 572:65-85. [DOI: 10.1016/bs.mie.2016.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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32
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Abstract
The goal in fluorescence microscopy is to detect the signal of fluorescently labeled molecules with great sensitivity and minimal background noise. In epifluorescence microscopy, it is difficult to observe weak signals along the optical axis, owing to the overpowering signal from the out-of-focus particles. Confocal microscopy uses a small pinhole to produce thin optical sections (∼500 nm), but the pinhole rejects some of the in-focus photons as well. Total internal reflection fluorescence microscopy (TIRFM) is a wide-field illumination technique that illuminates only the molecules near the glass coverslip. It has become widely used in biological imaging because it has a significantly reduced background and high temporal resolution capability. TIRFM has been used to study proteins in vitro as well as signaling cascades by hormones and neurotransmitters, intracellular cargo transport, actin dynamics near the plasma membrane, and focal adhesions in living cells. Because TIRF illumination is restricted to the glass-water interface and does not penetrate the specimen, it is well suited for studying the interaction of molecules within or near the cell membrane in living cells.
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33
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Guyer CA, Tao S. Total internal reflection fluorescence spectrometry using a dual optical fiber sample cell. APPLIED SPECTROSCOPY 2015; 69:608-612. [PMID: 25815794 DOI: 10.1366/14-07744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A novel total internal reflection fluorescence (TIRF) spectrometric technique using a dual optical fiber sample cell was developed. A conventional silica optical fiber was used for exciting fluorescence compounds in its evanescent wave field. A liquid core waveguide (LCW) was used to collect the fluorescence photons emitted from fluorescence compounds existing in an excitation fiber's evanescent wave field. The collected fluorescence photons were guided through the LCW and sent to a fluorescence spectrometer for detection. The spatial separation of excitation light and fluorescence light reduces the excitation-light-related optical noise signal, which is the major factor limiting fluorescence techniques from achieving lower detection limit. Preliminary results obtained from this work indicate that the optical fiber TIRF system of this work can detect 4.6*10(-18) mole rhodamine 6G (2.7*10(6) molecules) existing in the evanescent wave field of the excitation optical fiber.
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34
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DeWitt M, Schenkel T, Yildiz A. Fluorescence tracking of motor proteins in vitro. ACTA ACUST UNITED AC 2014; 105:211-34. [PMID: 25095997 DOI: 10.1007/978-3-0348-0856-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Motor proteins convert the chemical energy of adenosine triphosphate (ATP) hydrolysis into directed movement along filamentous tracks, such as DNA, microtubule, and actin. The motile properties of motors are essential to their wide variety of cellular functions, including cargo transport, mitosis, cell motility, nuclear positioning, and ciliogenesis. Detailed understanding of the biophysical mechanisms of motor motility is therefore essential to understanding the physical basis of these processes. In which direction is the motor going? How fast and how far can a single motor walk down its track? How is ATP hydrolysis coupled to directed motion? How do multiple subunits of a motor coordinate with each other during motility? These questions can be addressed directly by tracking motors at a single-molecule level. This chapter will focus on high-resolution fluorescence tracking techniques of the processive cytoskeletal motors: myosins, kinesins, and cytoplasmic dynein. We outline the theoretical and practical considerations for studying these motors in vitro using fluorescence tracking at nanometer precision.
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Affiliation(s)
- Mark DeWitt
- Biophysics Graduate Group and Physics Department, University of California, Berkeley, CA, 94720, USA
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35
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Tracking single molecules at work in living cells. Nat Chem Biol 2014; 10:524-32. [PMID: 24937070 DOI: 10.1038/nchembio.1558] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/21/2014] [Indexed: 11/09/2022]
Abstract
Methods for imaging and tracking single molecules conjugated with fluorescent probes, called single-molecule tracking (SMT), are now providing researchers with the unprecedented ability to directly observe molecular behaviors and interactions in living cells. Current SMT methods are achieving almost the ultimate spatial precision and time resolution for tracking single molecules, determined by the currently available dyes. In cells, various molecular interactions and reactions occur as stochastic and probabilistic processes. SMT provides an ideal way to directly track these processes by observing individual molecules at work in living cells, leading to totally new views of the biochemical and molecular processes used by cells whether in signal transduction, gene regulation or formation and disintegration of macromolecular complexes. Here we review SMT methods, summarize the recent results obtained by SMT, including related superresolution microscopy data, and describe the special concerns when SMT applications are shifted from the in vitro paradigms to living cells.
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36
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Shen H, Huang E, Das T, Xu H, Ellisman M, Liu Z. TIRF microscopy with ultra-short penetration depth. OPTICS EXPRESS 2014; 22:10728-10734. [PMID: 24921774 DOI: 10.1364/oe.22.010728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRF), in both commercial and custom-built configurations, is widely used for high signal-noise ratio imaging. The imaging depth of traditional TIRF is sensitive to the incident angle of the laser, and normally limited to around 100 nm. In our paper, using a high refractive index material and the evanescent waves of various waveguide modes, we propose a compact and tunable ultra-short decay length TIRF system, which can reach decay lengths as short as 19 nm, and demonstrate its application for imaging fluorescent dye-labeled F-actin in HeLa cells.
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37
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Lin D, Huang JS. Slant-gap plasmonic nanoantennas for optical chirality engineering and circular dichroism enhancement. OPTICS EXPRESS 2014; 22:7434-45. [PMID: 24718118 DOI: 10.1364/oe.22.007434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We present a new design of plasmonic nanoantenna with slant gap for optical chirality engineering. At resonance, the slant gap provides highly enhanced electric field parallel to external magnetic field with a phase delay of π/2, resulting in enhanced optical chirality. We show by numerical simulations that upon linearly polarized excitation our nanoantenna can generate near field with enhanced optical chirality which can be tuned by the slant angle and resonance condition. Our design allows chiral analysis with linearly polarized light and may find applications in circular dichroism analysis of chiral matter at surface.
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38
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Fukuoka H, Sagawa T, Inoue Y, Takahashi H, Ishijima A. Direct Imaging of Intracellular Signaling Components That Regulate Bacterial Chemotaxis. Sci Signal 2014; 7:ra32. [DOI: 10.1126/scisignal.2004963] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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39
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ATP turnover by individual myosin molecules hints at two conformers of the myosin active site. Proc Natl Acad Sci U S A 2014; 111:2536-41. [PMID: 24550279 DOI: 10.1073/pnas.1316390111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coupling of ATP hydrolysis to structural changes in the motor domain is fundamental to the driving of motile functions by myosins. Current understanding of this chemomechanical coupling is primarily based on ensemble average measurements in solution and muscle fibers. Although important, the averaging could potentially mask essential details of the chemomechanical coupling, particularly for mixed populations of molecules. Here, we demonstrate the potential of studying individual myosin molecules, one by one, for unique insights into established systems and to dissect mixed populations of molecules where separation can be particularly challenging. We measured ATP turnover by individual myosin molecules, monitoring appearance and disappearance of fluorescent spots upon binding/dissociation of a fluorescent nucleotide to/from the active site of myosin. Surprisingly, for all myosins tested, we found two populations of fluorescence lifetimes for individual myosin molecules, suggesting that termination of fluorescence occurred by two different paths, unexpected from standard kinetic schemes of myosin ATPase. In addition, molecules of the same myosin isoform showed substantial intermolecular variability in fluorescence lifetimes. From kinetic modeling of our two fluorescence lifetime populations and earlier solution data, we propose two conformers of the active site of myosin, one that allows the complete ATPase cycle and one that dissociates ATP uncleaved. Statistical analysis and Monte Carlo simulations showed that the intermolecular variability in our studies is essentially due to the stochastic behavior of enzyme kinetics and the limited number of ATP binding events detectable from an individual myosin molecule with little room for static variation among individual molecules, previously described for other enzymes.
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Karagiannis P, Ishii Y, Yanagida T. Molecular machines like myosin use randomness to behave predictably. Chem Rev 2014; 114:3318-34. [PMID: 24484383 DOI: 10.1021/cr400344n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Karagiannis
- Quantitative Biology Center, Riken (QBiC) , Furuedai 6-2-3, Suita, Osaka 565-0874, Japan
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41
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Zhang H, Guo P. Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation. Methods 2014; 67:169-76. [PMID: 24440482 DOI: 10.1016/j.ymeth.2014.01.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/28/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022] Open
Abstract
Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry of molecules or subunits within biocomplexes or nanomachines at nanometer scales. Stoichiometry is determined by real-time observation of the number of descending steps resulted from the photobleaching of individual fluorophore. This technology has now been used extensively for single molecule counting of protein, RNA, and other macromolecules in a variety of complexes or nanostructures. Here, we elucidate the SMPB technology, using the counting of RNA molecules within a bacteriophage phi29 DNA-packaging biomotor as an example. The method described here can be applied to the single molecule counting of other molecules in other systems. The construction of a concise, simple and economical single molecule total internal reflection fluorescence (TIRF) microscope combining prism-type and objective-type TIRF is described. The imaging system contains a deep-cooled sensitive EMCCD camera with single fluorophore detection sensitivity, a laser combiner for simultaneous dual-color excitation, and a Dual-View™ imager to split the multiple outcome signals to different detector channels based on their wavelengths. Methodology of the single molecule photobleaching assay used to elucidate the stoichiometry of RNA on phi29 DNA packaging motor and the mechanism of protein/RNA interaction are described. Different methods for single fluorophore labeling of RNA molecules are reviewed. The process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is also described.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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Fukuda S, Uchihashi T, Iino R, Okazaki Y, Yoshida M, Igarashi K, Ando T. High-speed atomic force microscope combined with single-molecule fluorescence microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:073706. [PMID: 23902075 DOI: 10.1063/1.4813280] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
High-speed atomic force microscopy (HS-AFM) and total internal reflection fluorescence microscopy (TIRFM) have mutually complementary capabilities. Here, we report techniques to combine these microscopy systems so that both microscopy capabilities can be simultaneously used in the full extent. To combine the two systems, we have developed a tip-scan type HS-AFM instrument equipped with a device by which the laser beam from the optical lever detector can track the cantilever motion in the X- and Y-directions. This stand-alone HS-AFM system is mounted on an inverted optical microscope stage with a wide-area scanner. The capability of this combined system is demonstrated by simultaneous HS-AFM∕TIRFM imaging of chitinase A moving on a chitin crystalline fiber and myosin V walking on an actin filament.
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Affiliation(s)
- Shingo Fukuda
- Department of Physics, College of Science and Engineering, Kanazawa University, Ishikawa 920-1192, Japan
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43
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Liang Y, Cucchetti M, Roncagalli R, Yokosuka T, Malzac A, Bertosio E, Imbert J, Nijman IJ, Suchanek M, Saito T, Wülfing C, Malissen B, Malissen M. The lymphoid lineage-specific actin-uncapping protein Rltpr is essential for costimulation via CD28 and the development of regulatory T cells. Nat Immunol 2013; 14:858-66. [PMID: 23793062 DOI: 10.1038/ni.2634] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/01/2013] [Indexed: 02/07/2023]
Abstract
Although T cell activation can result from signaling via T cell antigen receptor (TCR) alone, physiological T cell responses require costimulation via the coreceptor CD28. Through the use of an N-ethyl-N-nitrosourea-mutagenesis screen, we identified a mutation in Rltpr. We found that Rltpr was a lymphoid cell-specific, actin-uncapping protein essential for costimulation via CD28 and the development of regulatory T cells. Engagement of TCR-CD28 at the immunological synapse resulted in the colocalization of CD28 with both wild-type and mutant Rltpr proteins. However, the connection between CD28 and protein kinase C-θ and Carma1, two key effectors of CD28 costimulation, was abrogated in T cells expressing mutant Rltpr, and CD28 costimulation did not occur in those cells. Our findings provide a more complete model of CD28 costimulation in which Rltpr has a key role.
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Affiliation(s)
- Yinming Liang
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille, France
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Ikezaki K, Komori T, Yanagida T. Spontaneous detachment of the leading head contributes to myosin VI backward steps. PLoS One 2013; 8:e58912. [PMID: 23527046 PMCID: PMC3601099 DOI: 10.1371/journal.pone.0058912] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/08/2013] [Indexed: 11/23/2022] Open
Abstract
Myosin VI is an ATP driven molecular motor that normally takes forward and processive steps on actin filaments, but also on occasion stochastic backward steps. While a number of models have attempted to explain the backwards steps, none offer an acceptable mechanism for their existence. We therefore performed single molecule imaging of myosin VI and calculated the stepping rates of forward and backward steps at the single molecule level. The forward stepping rate was proportional to the ATP concentration, whereas the backward stepping rate was independent. Using these data, we proposed that spontaneous detachment of the leading head is uncoupled from ATP binding and is responsible for the backward steps of myosin VI.
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Affiliation(s)
- Keigo Ikezaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan
| | - Tomotaka Komori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan
- * E-mail: (TK); (TY)
| | - Toshio Yanagida
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan
- Center for Information and Neural Networks (CiNet), Suita, Osaka, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- * E-mail: (TK); (TY)
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45
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ABCA1 dimer-monomer interconversion during HDL generation revealed by single-molecule imaging. Proc Natl Acad Sci U S A 2013; 110:5034-9. [PMID: 23479619 DOI: 10.1073/pnas.1220703110] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The generation of high-density lipoprotein (HDL), one of the most critical events for preventing atherosclerosis, is mediated by ATP-binding cassette protein A1 (ABCA1). ABCA1 is known to transfer cellular cholesterol and phospholipids to apolipoprotein A-I (apoA-I) for generating discoidal HDL (dHDL) particles, composed of 100-200 lipid molecules surrounded by two apoA-I molecules; however, the regulatory mechanisms are still poorly understood. Here we observed ABCA1-GFP and apoA-I at the level of single molecules on the plasma membrane via a total internal reflection fluorescence microscope. We found that about 70% of total ABCA1-GFP spots are immobilized on the plasma membrane and estimated that about 89% of immobile ABCA1 molecules are in dimers. Furthermore, an ATPase-deficient ABCA1 mutant failed to be immobilized or form a dimer. We found that the lipid acceptor apoA-I interacts with the ABCA1 dimer to generate dHDL and is followed by ABCA1 dimer-monomer interconversion. This indicates that the formation of the ABCA1 dimer is the key for apoA-I binding and nascent HDL generation. Our findings suggest the physiological significance of conversion of the ABCA1 monomer to a dimer: The dimer serves as a receptor for two apoA-I molecules for dHDL particle generation.
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46
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Hu J, Zhang CY. Simple and Accurate Quantification of Quantum Yield at the Single-Molecule/Particle Level. Anal Chem 2013; 85:2000-4. [DOI: 10.1021/ac3036487] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Hu
- Single-Molecule Detection and Imaging Laboratory, Shenzhen
Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory, Shenzhen
Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
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Kong SG, Arai Y, Suetsugu N, Yanagida T, Wada M. Rapid severing and motility of chloroplast-actin filaments are required for the chloroplast avoidance response in Arabidopsis. THE PLANT CELL 2013; 25:572-90. [PMID: 23404888 PMCID: PMC3608779 DOI: 10.1105/tpc.113.109694] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 01/16/2013] [Accepted: 01/20/2013] [Indexed: 05/20/2023]
Abstract
Phototropins (phot1 and phot2 in Arabidopsis thaliana) relay blue light intensity information to the chloroplasts, which move toward weak light (the accumulation response) and away from strong light (the avoidance response). Chloroplast-actin (cp-actin) filaments are vital for mediating these chloroplast photorelocation movements. In this report, we examine in detail the cp-actin filament dynamics by which the chloroplast avoidance response is regulated. Although stochastic dynamics of cortical actin fragments are observed on the chloroplasts, the basic mechanisms underlying the disappearance (including severing and turnover) of the cp-actin filaments are regulated differently from those of cortical actin filaments. phot2 plays a pivotal role in the strong blue light-induced severing and random motility of cp-actin filaments, processes that are therefore essential for asymmetric cp-actin formation for the avoidance response. In addition, phot2 functions in the bundling of cp-actin filaments that is induced by dark incubation. By contrast, the function of phot1 is dispensable for these responses. Our findings suggest that phot2 is the primary photoreceptor involved in the rapid reorganization of cp-actin filaments that allows chloroplasts to change direction rapidly and control the velocity of the avoidance movement according to the light's intensity and position.
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Affiliation(s)
- Sam-Geun Kong
- Department of Biology, Graduate School of Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yoshiyuki Arai
- Laboratories for Nanobiology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Noriyuki Suetsugu
- Department of Biology, Graduate School of Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Toshio Yanagida
- Laboratories for Nanobiology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masamitsu Wada
- Department of Biology, Graduate School of Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
- Address correspondence to
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48
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Elting MW, Leslie SR, Churchman LS, Korlach J, McFaul CMJ, Leith JS, Levene MJ, Cohen AE, Spudich JA. Single-molecule fluorescence imaging of processive myosin with enhanced background suppression using linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC). OPTICS EXPRESS 2013; 21:1189-202. [PMID: 23389011 PMCID: PMC3632498 DOI: 10.1364/oe.21.001189] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/14/2012] [Accepted: 12/15/2012] [Indexed: 05/22/2023]
Abstract
Resolving single fluorescent molecules in the presence of high fluorophore concentrations remains a challenge in single-molecule biophysics that limits our understanding of weak molecular interactions. Total internal reflection fluorescence (TIRF) imaging, the workhorse of single-molecule fluorescence microscopy, enables experiments at concentrations up to about 100 nM, but many biological interactions have considerably weaker affinities, and thus require at least one species to be at micromolar or higher concentration. Current alternatives to TIRF often require three-dimensional confinement, and thus can be problematic for extended substrates, such as cytoskeletal filaments. To address this challenge, we have demonstrated and applied two new single-molecule fluorescence microscopy techniques, linear zero-mode waveguides (ZMWs) and convex lens induced confinement (CLIC), for imaging the processive motion of molecular motors myosin V and VI along actin filaments. Both technologies will allow imaging in the presence of higher fluorophore concentrations than TIRF microscopy. They will enable new biophysical measurements of a wide range of processive molecular motors that move along filamentous tracks, such as other myosins, dynein, and kinesin. A particularly salient application of these technologies will be to examine chemomechanical coupling by directly imaging fluorescent nucleotide molecules interacting with processive motors as they traverse their actin or microtubule tracks.
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Affiliation(s)
- Mary Williard Elting
- Department of Applied Physics, Stanford University, Stanford, California 94305,
USA
- Department of Biochemistry, Stanford University, Stanford, California 94305,
USA
- Current Address: Department of Cell and Tissue Biology, University of California, San Francisco, California 94143,
USA
| | - Sabrina R. Leslie
- Department of Physics, McGill University, Montreal, QC H3A 2TA,
Canada
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, Massachusetts 02138,
USA
| | - L. Stirling Churchman
- Department of Biochemistry, Stanford University, Stanford, California 94305,
USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115,
USA
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025,
USA
| | | | - Jason S. Leith
- Department of Physics, McGill University, Montreal, QC H3A 2TA,
Canada
| | - Michael J. Levene
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520,
USA
| | - Adam E. Cohen
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, Massachusetts 02138,
USA
| | - James A. Spudich
- Department of Biochemistry, Stanford University, Stanford, California 94305,
USA
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49
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Lee S, Kang SH. Quenching effect on gold nano-patterned cardiac troponin I chip by total internal reflection fluorescence microscopy. Talanta 2013; 104:32-8. [DOI: 10.1016/j.talanta.2012.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 11/26/2022]
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50
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Suzuki KGN, Kasai RS, Fujiwara TK, Kusumi A. Single-molecule imaging of receptor-receptor interactions. Methods Cell Biol 2013; 117:373-90. [PMID: 24143988 DOI: 10.1016/b978-0-12-408143-7.00020-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-molecule imaging is a powerful tool for the study of dynamic molecular interactions in living cell plasma membranes. Herein, we describe a single-molecule imaging microscopy technique that can be used to measure lifetimes and densities of receptor dimers and oligomers. This method can be performed using a total internal reflection fluorescent microscope equipped with one or two high-sensitivity cameras. For dual-color observation, two images obtained synchronously in different colors are spatially corrected and then overlaid. Receptors must be expressed at low density in cell plasma membranes because high-density expression (>2 molecules/μm(2)) creates difficulty for tracking individual fluorescent spots. In addition, the receptors should be labeled with highly photostable fluorophores at high efficiency because short photobleaching lifetimes and low labeling efficiency of receptors reduce the probability of detecting dimers and oligomers. In this chapter, we describe methods for observing and detecting colocalization of the individual fluorescent spots of receptors labeled with fluorophores via small tags and the estimation of true dimer and oligomer lifetimes after correction with photobleaching lifetimes of fluorophores.
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Affiliation(s)
- Kenichi G N Suzuki
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan; National Centre for Biological Sciences (NCBS)/Institute for Stem Cell Biology and Regenerative Medicine (inStem), Bangalore, India
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