1
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Kim GW, Ha JW. Direct Observation of In-Focus Plasmonic Cargos via Breaking Angular Degeneracy in Differential Interference Contrast Microscopy. JACS AU 2023; 3:3436-3445. [PMID: 38155657 PMCID: PMC10751767 DOI: 10.1021/jacsau.3c00594] [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: 10/03/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
Breaking the angular degeneracy arising from the 2-fold optical symmetry of plasmonic anisotropic nanoprobes is critical in biological studies. In this study, we propose differential interference contrast (DIC) microscopy-based focused orientation and position imaging (dFOPI) to break the angular degeneracy of single gold nanorods (AuNRs). Single in-focus AuNRs (39 nm × 123 nm) within a spherical mesoporous silica shell were characterized with high throughput and produced distinct doughnut-shaped DIC image patterns featuring two lobes in the peripheral region, attributed to the scattering contribution of the AuNRs with large scattering cross sections. Interestingly, rotation of the lobes was observed in the focal plane for a large AuNR (>100 nm) tilted by more than ∼20° from the horizontal plane as the rotational stage was moved by 10° in a rotational study. From the rotation-dependent characteristic patterns, we directly visualized counterclockwise/clockwise rotations without the angular degeneracy at the localized surface plasmon resonance wavelength. Therefore, our dFOPI method can be applied for in vivo studies of important biological systems. To validate this claim, we tracked the three-dimensional rotational behavior of transferrin-modified in-focus AuNRs during clathrin-mediated endocytosis in real time without sacrificing the temporal and spatial resolution. In the invagination and scission stage, one or two directed twist motions of the AuNR cargos detached the AuNR-containing vesicles from the cell membrane. Furthermore, the dFOPI method directly visualized and revealed the right-handed twisting action along the dynamin helix in dynamin-catalyzed fission in live cells.
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Affiliation(s)
- Geun Wan Kim
- Department
of Chemistry, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, South Korea
| | - Ji Won Ha
- Department
of Chemistry, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, South Korea
- Energy
Harvest-Storage Research Center (EHSRC), University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, South Korea
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2
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Xue J, Wang Z, Zhang H, He Y. Viscosity Measurement in Biocondensates Using Deep-Learning-Assisted Single-Particle Rotational Analysis. J Phys Chem B 2022; 126:7541-7551. [PMID: 36129778 DOI: 10.1021/acs.jpcb.2c03243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Viscoelastic characterization is of great importance for the investigation of biomolecular condensates. Single-particle-tracking-based rotational diffusion analysis of single nanorods is an effective approach for quantitative viscosity measurement. However, in the case of high background and noise with high-speed image acquisition, accurate extraction of diffusivity from the data is a challenging task. Here, we develop a novel frequency-domain-based deep learning (DL) method for single nanorod rotational tracking analysis. We synthesized Brownian rotational time-series data for training, designed a data preprocessing module to reduce the effect of noise, and extracted rotational diffusion coefficient using recurrent neural networks in the frequency domain. Compared with the traditional curve-fitting-based methods, our method shows higher accuracy and a wider detection range for viscosity measurement. We verified our method using experimental data from plasmonic imaging of single gold nanorods (AuNRs) in glycerol solution and PGL droplets. Our method can be potentially applied to the viscosity measurement of different biomolecular condensates in vitro and in vivo.
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Affiliation(s)
- Jianfeng Xue
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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3
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Wang Z, Chen D, Guan D, Liang X, Xue J, Zhao H, Song G, Lou J, He Y, Zhang H. Material properties of phase-separated TFEB condensates regulate the autophagy-lysosome pathway. J Biophys Biochem Cytol 2022; 221:213069. [PMID: 35293953 PMCID: PMC8931539 DOI: 10.1083/jcb.202112024] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/25/2022] [Accepted: 02/11/2022] [Indexed: 12/24/2022] Open
Abstract
Very little is known about how the material properties of protein condensates assembled via liquid–liquid phase separation (LLPS) are maintained and affect physiological functions. Here we show that liquid-like condensates of the transcription factor TFEB exhibit low fusion propensity in vitro and in living cells. We directly measured the attraction force between droplets, and we characterized the interfacial tension, viscosity, and elasticity of TFEB condensates. TFEB condensates contain rigid interfacial boundaries that govern their interaction behaviors. Several small molecules, including Ro-3306, modify the material properties of TFEB condensates, increasing their size and fusion propensity. These compounds promote lysosomal biogenesis and function in a TFEB-dependent manner without changing its cytoplasmic-nuclear translocation. Ro-3306 promotes autophagy activity, facilitating degradation of toxic protein aggregates. Our study helps explain how protein condensates are maintained as physically separate entities and reveals that the material properties of TFEB condensates can be harnessed to modulate TFEB activity.
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Affiliation(s)
- Zheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Di Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dongshi Guan
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Xiaobo Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianfeng Xue
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guangtao Song
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jizhong Lou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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4
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Single-Molecule Biophysical Techniques to Study Actomyosin Force Transduction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32451857 DOI: 10.1007/978-3-030-38062-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Inside the cellular environment, molecular motors can work in concert to conduct a variety of important physiological functions and processes that are vital for the survival of a cell. However, in order to decipher the mechanism of how these molecular motors work, single-molecule microscopy techniques have been popular methods to understand the molecular basis of the emerging ensemble behavior of these motor proteins.In this chapter, we discuss various single-molecule biophysical imaging techniques that have been used to expose the mechanics and kinetics of myosins. The chapter should be taken as a general overview and introductory guide to the many existing techniques; however, since other chapters will discuss some of these techniques more thoroughly, the readership should refer to those chapters for further details and discussions. In particular, we will focus on scattering-based single-molecule microscopy methods, some of which have become more popular in the recent years and around which the work in our laboratories has been centered.
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5
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Song L, Feng Y, Guo X, Shen Y, Wu D, Wu Z, Zhou C, Zhu L, Gao S, Liu W, Zhang X, Li Z. Ultrafast polarization bio-imaging based on coherent detection and time-stretch techniques. BIOMEDICAL OPTICS EXPRESS 2018; 9:6556-6568. [PMID: 31065449 PMCID: PMC6490988 DOI: 10.1364/boe.9.006556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 06/09/2023]
Abstract
Optical polarization imaging has played an important role in many biological and biomedical applications, as it provides a label-free and non-invasive detection scheme to reveal the polarization information of optical rotation, birefringence, and photoelasticity distribution inherent in biological samples. However, the imaging speeds of the previously demonstrated polarization imaging techniques were often limited by the slow frame rates of the arrayed imaging detectors, which usually run at frame rates of several hundred hertz. By combining the optical coherent detection of orthogonal polarizations and the optical time-stretch imaging technique, we achieved ultrafast polarization bio-imaging at an extremely fast record line scanning rate up to 100 MHz without averaging. We experimentally demonstrated the superior performance of our method by imaging three slices of different kinds of biological samples with the retrieved Jones matrix and polarization-sensitive information including birefringence and diattenuation. The proposed system in this paper may find potential applications for ultrafast polarization dynamics in living samples or some other advanced biomedical research.
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Affiliation(s)
- Lu Song
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Yuanhua Feng
- Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaojie Guo
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Yuecheng Shen
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Daixuan Wu
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhenhua Wu
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 510632, China
| | - Congran Zhou
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Linyan Zhu
- Department of Pharmacology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Shecheng Gao
- Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou 510632, China
| | - Weiping Liu
- Department of Electronic Engineering, College of Information Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xuming Zhang
- Department of Applied Physics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Zhaohui Li
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
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6
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van Mameren J, Vermeulen K, Wuite GJL, Peterman EJG. A polarized view on DNA under tension. J Chem Phys 2018; 148:123306. [PMID: 29604805 DOI: 10.1063/1.5004019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of double-stranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.
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Affiliation(s)
- Joost van Mameren
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Karen Vermeulen
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
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7
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Dunstone MA, de Marco A. Cryo-electron tomography: an ideal method to study membrane-associated proteins. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630150 DOI: 10.1098/rstb.2016.0210] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) is a three-dimensional imaging technique that makes it possible to analyse the structure of complex and dynamic biological assemblies in their native conditions. The latest technological and image processing developments demonstrate that it is possible to obtain structural information at nanometre resolution. The sample preparation required for the cryo-ET technique does not require the isolation of a protein and other macromolecular complexes from its native environment. Therefore, cryo-ET is emerging as an important tool to study the structure of membrane-associated proteins including pores.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Michelle A Dunstone
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia.,Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia .,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia
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8
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Fu G, Tu LC, Zilman A, Musser SM. Investigating molecular crowding within nuclear pores using polarization-PALM. eLife 2017; 6:e28716. [PMID: 28949296 PMCID: PMC5693140 DOI: 10.7554/elife.28716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/25/2017] [Indexed: 12/25/2022] Open
Abstract
The key component of the nuclear pore complex (NPC) controlling permeability, selectivity, and the speed of nucleocytoplasmic transport is an assembly of natively unfolded polypeptides, which contain phenylalanine-glycine (FG) binding sites for nuclear transport receptors. The architecture and dynamics of the FG-network have been refractory to characterization due to the paucity of experimental methods able to probe the mobility and density of the FG-polypeptides and embedded macromolecules within intact NPCs. Combining fluorescence polarization, super-resolution microscopy, and mathematical analyses, we examined the rotational mobility of fluorescent probes at various locations within the FG-network under different conditions. We demonstrate that polarization PALM (p-PALM) provides a rich source of information about low rotational mobilities that are inaccessible with bulk fluorescence anisotropy approaches, and anticipate that p-PALM is well-suited to explore numerous crowded cellular environments. In total, our findings indicate that the NPC's internal organization consists of multiple dynamic environments with different local properties.
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Affiliation(s)
- Guo Fu
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
| | - Li-Chun Tu
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
| | - Anton Zilman
- Department of PhysicsUniversity of TorontoTorontoCanada
- Institute for Biomaterials and Biomedical EngineeringUniversity of TorontoTorontoCanada
| | - Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of MedicineThe Texas A&M University Health Science CenterCollege StationUnited States
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9
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Shroder DY, Lippert LG, Goldman YE. Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl Fluoresc 2016; 4:042004. [PMID: 28192292 PMCID: PMC5308470 DOI: 10.1088/2050-6120/4/4/042004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.
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10
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Krause S, Neumann M, Fröbe M, Magerle R, von Borczyskowski C. Monitoring Nanoscale Deformations in a Drawn Polymer Melt with Single-Molecule Fluorescence Polarization Microscopy. ACS NANO 2016; 10:1908-1917. [PMID: 26831762 DOI: 10.1021/acsnano.5b05729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Elongating a polymer melt causes polymer segments to align and polymer coils to deform along the drawing direction. Despite the importance of this molecular response for understanding the viscoelastic properties and relaxation behavior of polymeric materials, studies on the single-molecule level are rare and were not performed in real time. Here we use single-molecule fluorescence polarization microscopy for monitoring the position and orientation of single fluorescent perylene diimide molecules embedded in a free-standing thin film of a polymethyl acrylate (PMA) melt with a time resolution of 500 ms during the film drawing and the subsequent stress relaxation period. The orientation distribution of the perylene diimide molecules is quantitatively described with a model of rod-like objects embedded in a uniaxially elongated matrix. The orientation of the fluorescent probe molecules is directly coupled to the local deformation of the PMA melt, which we derive from the distances between individual dye molecules. In turn, the fluorescence polarization monitors the shape deformation of the polymer coils on a length scale of 5 nm. During stress relaxation, the coil shape relaxes four times more slowly than the mechanical stress. This shows that stress relaxation involves processes on length scales smaller than a polymer coil. Our work demonstrates how optical spectroscopy and microscopy can be used to study the coupling of individual fluorescent probe molecules to their embedding polymeric matrix and to an external mechanical stimulus on the single-molecule level.
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Affiliation(s)
- Stefan Krause
- Fakultät für Naturwissenschaften, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Martin Neumann
- Fakultät für Naturwissenschaften, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Melanie Fröbe
- Fakultät für Naturwissenschaften, Technische Universität Chemnitz , 09107 Chemnitz, Germany
| | - Robert Magerle
- Fakultät für Naturwissenschaften, Technische Universität Chemnitz , 09107 Chemnitz, Germany
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11
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Quantitative nanoscale imaging of orientational order in biological filaments by polarized superresolution microscopy. Proc Natl Acad Sci U S A 2016; 113:E820-8. [PMID: 26831082 DOI: 10.1073/pnas.1516811113] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Essential cellular functions as diverse as genome maintenance and tissue morphogenesis rely on the dynamic organization of filamentous assemblies. For example, the precise structural organization of DNA filaments has profound consequences on all DNA-mediated processes including gene expression, whereas control over the precise spatial arrangement of cytoskeletal protein filaments is key for mechanical force generation driving animal tissue morphogenesis. Polarized fluorescence is currently used to extract structural organization of fluorescently labeled biological filaments by determining the orientation of fluorescent labels, however with a strong drawback: polarized fluorescence imaging is indeed spatially limited by optical diffraction, and is thus unable to discriminate between the intrinsic orientational mobility of the fluorophore labels and the real structural disorder of the labeled biomolecules. Here, we demonstrate that quantitative single-molecule polarized detection in biological filament assemblies allows not only to correct for the rotational flexibility of the label but also to image orientational order of filaments at the nanoscale using superresolution capabilities. The method is based on polarized direct stochastic optical reconstruction microscopy, using dedicated optical scheme and image analysis to determine both molecular localization and orientation with high precision. We apply this method to double-stranded DNA in vitro and microtubules and actin stress fibers in whole cells.
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12
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Blythe KL, Titus EJ, Willets KA. Objective-Induced Point Spread Function Aberrations and Their Impact on Super-Resolution Microscopy. Anal Chem 2015; 87:6419-24. [PMID: 26011175 DOI: 10.1021/acs.analchem.5b01848] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This study demonstrates how different microscope objectives can lead to asymmetric imaging aberrations in the point spread function of dipolar emitters, which can adversely affect the quality of fit in super-resolution imaging. Luminescence from gold nanorods was imaged with four different objectives to measure the diffraction-limited emission and characterize deviations from the expected dipolar emission patterns. Each luminescence image was fit to a three-dipole emission model to generate fit residuals that visually relay aberrations in the point spread function caused by the different microscope objectives. Output parameters from the fit model were compared to experimentally measured values, and we find that while some objectives provide high quality fits across all nanorods studied, others show significant aberrations and are inappropriate for super-resolution imaging. This work presents a simple and robust strategy for quickly assessing the quality of point spread functions produced by different microscope objectives.
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Affiliation(s)
- Karole L Blythe
- Department of Chemistry, The University of Texas at Austin, 102 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Eric J Titus
- Department of Chemistry, The University of Texas at Austin, 102 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Katherine A Willets
- Department of Chemistry, The University of Texas at Austin, 102 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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13
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Fang Y. Total internal reflection fluorescence quantification of receptor pharmacology. BIOSENSORS-BASEL 2015; 5:223-40. [PMID: 25922915 PMCID: PMC4493547 DOI: 10.3390/bios5020223] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 12/30/2022]
Abstract
Total internal reflection fluorescence (TIRF) microscopy has been widely used as a single molecule imaging technique to study various fundamental aspects of cell biology, owing to its ability to selectively excite a very thin fluorescent volume immediately above the substrate on which the cells are grown. However, TIRF microscopy has found little use in high content screening due to its complexity in instrumental setup and experimental procedures. Inspired by the recent demonstration of label-free evanescent wave biosensors for cell phenotypic profiling and drug screening with high throughput, we had hypothesized and demonstrated that TIRF imaging is also amenable to receptor pharmacology profiling. This paper reviews key considerations and recent applications of TIRF imaging for pharmacology profiling.
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Affiliation(s)
- Ye Fang
- Biochemical Technologies, Science and Technology Division, Corning Incorporated, Corning, NY 14831, USA.
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14
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Lu M, Lu HP. Probing protein multidimensional conformational fluctuations by single-molecule multiparameter photon stamping spectroscopy. J Phys Chem B 2014; 118:11943-55. [PMID: 25222115 PMCID: PMC4199541 DOI: 10.1021/jp5081498] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Conformational motions of proteins
are highly dynamic and intrinsically
complex. To capture the temporal and spatial complexity of conformational
motions and further to understand their roles in protein functions,
an attempt is made to probe multidimensional conformational dynamics
of proteins besides the typical one-dimensional FRET coordinate or
the projected conformational motions on the one-dimensional FRET coordinate.
T4 lysozyme hinge-bending motions between two domains along α-helix
have been probed by single-molecule FRET. Nevertheless, the domain
motions of T4 lysozyme are rather complex involving multiple coupled
nuclear coordinates and most likely contain motions besides hinge-bending.
It is highly likely that the multiple dimensional protein conformational
motions beyond the typical enzymatic hinged-bending motions have profound
impact on overall enzymatic functions. In this report, we have developed
a single-molecule multiparameter photon stamping spectroscopy integrating
fluorescence anisotropy, FRET, and fluorescence lifetime. This spectroscopic
approach enables simultaneous observations of both FRET-related site-to-site
conformational dynamics and molecular rotational (or orientational)
motions of individual Cy3-Cy5 labeled T4 lysozyme molecules. We have
further observed wide-distributed rotational flexibility along orientation
coordinates by recording fluorescence anisotropy and simultaneously
identified multiple intermediate conformational states along FRET
coordinate by monitoring time-dependent donor lifetime, presenting
a whole picture of multidimensional conformational dynamics in the
process of T4 lysozyme open-close hinge-bending enzymatic turnover
motions under enzymatic reaction conditions. By analyzing the autocorrelation
functions of both lifetime and anisotropy trajectories, we have also
observed the dynamic and static inhomogeneity of T4 lysozyme multidimensional
conformational fluctuation dynamics, providing a fundamental understanding
of the enzymatic reaction turnover dynamics associated with overall
enzyme as well as the specific active-site conformational fluctuations
that are not identifiable and resolvable in the conventional ensemble-averaged
experiment.
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Affiliation(s)
- Maolin Lu
- Center for Photochemical Sciences, Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
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15
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Ho SL, Chan HM, Ha AWY, Wong RNS, Li HW. Direct quantification of circulating miRNAs in different stages of nasopharyngeal cancerous serum samples in single molecule level with total internal reflection fluorescence microscopy. Anal Chem 2014; 86:9880-6. [PMID: 25207668 DOI: 10.1021/ac5025182] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate human gene expression at the post-transcriptional level. Growing evidence indicates that the expression profile of miRNAs is highly correlated with the occurrence of human diseases including cancers. Playing important roles in complex gene regulation processes, the aberrant expression pattern of various miRNAs is implicated in different types and even stages of cancer. Besides localizing in cells, many of these miRNAs are found circulating around the body in a wide variety of fluids such as urine, serum and saliva. Surprisingly, these extracellular circulating miRNAs are highly stable and resistant to degradation, and therefore, are considered as promising biomarkers for early cancer diagnostic via noninvasive extraction from body fluids. Unfortunately, the abundance of these small RNAs is ultralow in the body fluids, making it challenging to quantify them in complex sample matrixes. Establishing a sensitive, specific yet simple assay for an accurate quantification of circulating miRNAs is therefore desirable. Our group previously reported a sensitive and specific detection assay of miRNAs in single molecule level with the aid of total internal reflection fluorescence microscopy. In this work, we advanced the assay to differentiate the expression of a nasopharyngeal carcinoma (NPC) up-regulator hsa-mir-205 (mir-205) in serum collected from patients of different stages of NPC. To overcome the background matrix interference in serum, a locked nucleic acid-modified molecular beacon (LNA/MB) was applied as the detection probe to hybridize, capture and detect target mir-205 in serum matrix with enhanced sensitivity and specificity. A detection limit of 500 fM was achieved. The as-developed method was capable of differentiating NPC stages by the level of mir-205 quantified in serum with only 10 μL of serum and the whole assay can be completed in 1 h. The experimental results agreed well with those previously reported whereas the quantity of miR-205 determined by our assay was found comparable to that of quantitative reverse transcription polymerase chain reaction (qRT-PCR), supporting that this assay can be served as a promising noninvasive detection tool for early NPC diagnosis, monitoring and staging.
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Affiliation(s)
- See-Lok Ho
- Department of Chemistry, Hong Kong Baptist University , Kowloon Tong, Hong Kong, People's Republic of China
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16
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Knight AE. Single-molecule fluorescence imaging by total internal reflection fluorescence microscopy (IUPAC Technical Report). PURE APPL CHEM 2014. [DOI: 10.1515/pac-2012-0605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractTotal internal reflection fluorescence (TIRF) is a popular illumination technique in microscopy, with many applications in cell and molecular biology and biophysics. The chief advantage of the technique is the high contrast that can be achieved by restricting fluorescent excitation to a thin layer. We summarise the optical theory needed to understand the technique and various aspects required for a practical implementation of it, including the merits of different TIRF geometries. Finally, we discuss a variety of applications including super-resolution microscopy and high-throughput DNA sequencing technologies.
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Affiliation(s)
- Alex E. Knight
- 1Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
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17
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Araghi HY, Giri NK, Paige MF. Polarized fluorescence microscopy analysis of patterned, polymerized perfluorotetradecanoic acid-pentacosadiynoic acid thin films. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 129:339-344. [PMID: 24747858 DOI: 10.1016/j.saa.2014.03.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/13/2014] [Accepted: 03/20/2014] [Indexed: 06/03/2023]
Abstract
Photoillumination of mixed films comprised of the photopolymerizable fatty acid 10,12 pentacosadiynoic acid and perfluorotetradecanoic acid deposited onto glass substrates gives rise to the formation of oriented polydiacetylene photopolymer fibers. The degree of polymer fiber orientation was investigated using dual-view, polarized fluorescence microscopy of the polydiacetylene, which allowed for characterization of individual fluorescent polymer fibers after photopolymerization, as well as comparison of the orientation of different fibers within the same sample. Measurements indicated that individual fibers consisted of multiple photopolymer strands with various orientations, and that there was a preferred orientation for fibers in the film as a whole. The fibers were preferentially oriented at an angle of approximately 60° to the direction of film compression during deposition from a Langmuir trough, with orientation being the result of mechanical stress exerted by the compression barriers coupled with rotation of the polymer fibers during film draining. These measurements were complemented with conventional "bulk" fluorescence polarization experiments, and compared with mixed film structures described previously for these systems at the air-water interface using Brewster angle microscopy.
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Affiliation(s)
| | - Neeraj K Giri
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Matthew F Paige
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada.
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18
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Xu D, He Y, Yeung ES. Direct Imaging of Transmembrane Dynamics of Single Nanoparticles with Darkfield Microscopy: Improved Orientation Tracking at Cell Sidewall. Anal Chem 2014; 86:3397-404. [DOI: 10.1021/ac403700u] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Dong Xu
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Yan He
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Edward S. Yeung
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Hunan University, Changsha, Hunan 410082, P. R. China
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19
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Hu Z, Adachi T, Lee YG, Haws RT, Hanson B, Ono RJ, Bielawski CW, Ganesan V, Rossky PJ, Vanden Bout DA. Effect of the side-chain-distribution density on the single-conjugated-polymer-chain conformation. Chemphyschem 2013; 14:4143-8. [PMID: 24243782 DOI: 10.1002/cphc.201300751] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/18/2013] [Indexed: 11/09/2022]
Abstract
The spatial arrangement of the side chains of conjugated polymer backbones has critical effects on the morphology and electronic and photophysical properties of the corresponding bulk films. The effect of the side-chain-distribution density on the conformation at the isolated single-polymer-chain level was investigated with regiorandom (rra-) poly(3-hexylthiophene) (P3HT) and poly(3-hexyl-2,5-thienylene vinylene) (P3HTV). Although pure P3HTV films are known to have low fluorescence quantum efficiencies, we observed a considerable increase in fluorescence intensity by dispersing P3HTV in poly(methyl methacrylate) (PMMA), which enabled a single-molecule spectroscopy investigation. With single-molecule fluorescence excitation polarization spectroscopy, we found that rra-P3HTV single molecules form highly ordered conformations. In contrast, rra-P3HT single molecules, display a wide variety of different conformations from isotropic to highly ordered, were observed. The experimental results are supported by extensive molecular dynamics simulations, which reveal that the reduced side-chain-distribution density, that is, the spaced-out side-chain substitution pattern, in rra-P3HTV favors more ordered conformations compared to rra-P3HT. Our results demonstrate that the distribution of side chains strongly affects the polymer-chain conformation, even at the single-molecule level, an aspect that has important implications when interpreting the macroscopic interchain packing structure exhibited by bulk polymer films.
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Affiliation(s)
- Zhongjian Hu
- Department of Chemistry and Biochemistry, University of Texas at Austin, 1 University Station A5300, Austin TX, 78712 (USA)
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20
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Bao J, Huck D, Gunther LK, Sellers JR, Sakamoto T. Actin structure-dependent stepping of myosin 5a and 10 during processive movement. PLoS One 2013; 8:e74936. [PMID: 24069366 PMCID: PMC3777900 DOI: 10.1371/journal.pone.0074936] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/07/2013] [Indexed: 11/22/2022] Open
Abstract
How myosin 10, an unconventional myosin, walks processively along actin is still controversial. Here, we used single molecule fluorescence techniques, TIRF and FIONA, to study the motility and the stepping mechanism of dimerized myosin 10 heavy-meromyosin-like fragment on both single actin filaments and two-dimensional F-actin rafts cross-linked by fascin or α-actinin. As a control, we also tracked and analyzed the stepping behavior of the well characterized processive motor myosin 5a. We have shown that myosin 10 moves processively along both single actin filaments and F-actin rafts with a step size of 31 nm. Moreover, myosin 10 moves more processively on fascin-F-actin rafts than on α-actinin-F-actin rafts, whereas myosin 5a shows no such selectivity. Finally, on fascin-F-actin rafts, myosin 10 has more frequent side steps to adjacent actin filaments than myosin 5a in the F-actin rafts. Together, these results reveal further single molecule features of myosin 10 on various actin structures, which may help to understand its cellular functions.
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Affiliation(s)
- Jianjun Bao
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
| | - Daniel Huck
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
| | - Laura K. Gunther
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
| | - James R. Sellers
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Takeshi Sakamoto
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, United States of America
- Department of Physiology, School of Medicine, Wayne State University, Detroit, Michigan, United States of America
- * E-mail:
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21
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Martin-Fernandez ML, Tynan CJ, Webb SED. A 'pocket guide' to total internal reflection fluorescence. J Microsc 2013; 252:16-22. [PMID: 23889125 PMCID: PMC4285862 DOI: 10.1111/jmi.12070] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 06/18/2013] [Indexed: 12/22/2022]
Abstract
The phenomenon of total internal reflection fluorescence (TIRF) was placed in the context of optical microscopy by Daniel Axelrod over three decades ago. TIRF microscopy exploits the properties of an evanescent electromagnetic field to optically section sample regions in the close vicinity of the substrate where the field is induced. The first applications in cell biology targeted investigation of phenomena at the basolateral plasma membrane. The most notable application of TIRF is single-molecule experiments, which can provide information on fluctuation distributions and rare events, yielding novel insights on the mechanisms governing the molecular interactions that underpin many fundamental processes within the cell. This short review intends to provide a ‘one stop shop’ explanation of the electromagnetic theory behind the remarkable properties of the evanescent field, guide the reader through the principles behind building or choosing your own TIRF system and consider how the most popular applications of the method exploit the evanescent field properties.
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Affiliation(s)
- M L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, UK
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22
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Berger CL. Breaking the millisecond barrier: single molecule motors wobble to find their next binding sites. Biophys J 2013; 104:1219-20. [PMID: 23528080 DOI: 10.1016/j.bpj.2013.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 02/12/2013] [Indexed: 11/17/2022] Open
Affiliation(s)
- Christopher L Berger
- Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT, USA.
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23
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Tilting and wobble of myosin V by high-speed single-molecule polarized fluorescence microscopy. Biophys J 2013; 104:1263-73. [PMID: 23528086 DOI: 10.1016/j.bpj.2013.01.057] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 12/23/2012] [Accepted: 01/28/2013] [Indexed: 01/07/2023] Open
Abstract
Myosin V is biomolecular motor with two actin-binding domains (heads) that take multiple steps along actin by a hand-over-hand mechanism. We used high-speed polarized total internal reflection fluorescence (polTIRF) microscopy to study the structural dynamics of single myosin V molecules that had been labeled with bifunctional rhodamine linked to one of the calmodulins along the lever arm. With the use of time-correlated single-photon counting technology, the temporal resolution of the polTIRF microscope was improved ~50-fold relative to earlier studies, and a maximum-likelihood, multitrace change-point algorithm was used to objectively determine the times when structural changes occurred. Short-lived substeps that displayed an abrupt increase in rotational mobility were detected during stepping, likely corresponding to random thermal fluctuations of the stepping head while it searched for its next actin-binding site. Thus, myosin V harnesses its fluctuating environment to extend its reach. Additional, less frequent angle changes, probably not directly associated with steps, were detected in both leading and trailing heads. The high-speed polTIRF method and change-point analysis may be applicable to single-molecule studies of other biological systems.
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24
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Marchuk K, Ha JW, Fang N. Three-dimensional high-resolution rotational tracking with superlocalization reveals conformations of surface-bound anisotropic nanoparticles. NANO LETTERS 2013; 13:1245-1250. [PMID: 23384297 DOI: 10.1021/nl304764w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The ability to directly follow three-dimensional rotational movement of anisotropic nanoparticles will greatly enhance our understanding of the way nanoparticles interact with surfaces. Herein, we demonstrate dual-color total internal reflection scattering microscopy as a tool to probe the interactions of plasmonic gold nanorods with functional surfaces. By taking advantage of both the short and long axis surface plasmon resonance scattering enhancement, we are able to decipher both in-plane and out-of-plane gold nanorod motion relative to the sample surface with equally high resolution. In combination with superlocalization through point spread function fitting, we overcome the four-quadrant angular degeneracy of gold nanorods in the focal plane of the objective and resolve conformations of surface-bound anisotropic nanoparticles in unprecedented detail.
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Affiliation(s)
- Kyle Marchuk
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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25
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Yip CM. Correlative optical and scanning probe microscopies for mapping interactions at membranes. Methods Mol Biol 2013; 950:439-56. [PMID: 23086889 DOI: 10.1007/978-1-62703-137-0_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Innovative approaches for real-time imaging on molecular-length scales are providing researchers with powerful strategies for characterizing molecular and cellular structures and dynamics. Combinatorial techniques that integrate two or more distinct imaging modalities are particularly compelling as they provide a means for overcoming the limitations of the individual modalities and, when applied simultaneously, enable the collection of rich multi-modal datasets. Almost since its inception, scanning probe microscopy has closely associated with optical microscopy. This is particularly evident in the fields of cellular and molecular biophysics where researchers are taking full advantage of these real-time, in situ, tools to acquire three-dimensional molecular-scale topographical images with nanometer resolution, while simultaneously characterizing their structure and interactions though conventional optical microscopy. The ability to apply mechanical or optical stimuli provides an additional experimental dimension that has shown tremendous promise for examining dynamic events on sub-cellular length scales. In this chapter, we describe recent efforts in developing these integrated platforms, the methodology for, and inherent challenges in, performing coupled imaging experiments, and the potential and future opportunities of these research tools for the fields of molecular and cellular biophysics with a specific emphasis on the application of these coupled approaches for the characterization of interactions occurring at membrane interfaces.
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Affiliation(s)
- Christopher M Yip
- Department of Chemical Engineering and Applied Chemistry, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
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26
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Ha JW, Marchuk K, Fang N. Focused orientation and position imaging (FOPI) of single anisotropic plasmonic nanoparticles by total internal reflection scattering microscopy. NANO LETTERS 2012; 12:4282-4288. [PMID: 22793645 DOI: 10.1021/nl301972t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The defocused orientation and position imaging (DOPI) and polarization-based in-focus imaging techniques have been widely used for detecting rotational motions with anisotropic gold nanorods (AuNRs) as orientation probes. However, these techniques have a number of significant limitations, such as the greatly reduced signal intensity and relatively low spatial and temporal resolutions for out-of-focus AuNRs and the angular degeneracy for in-focus AuNRs. Herein, we present a total internal reflection (TIR) scattering-based focused orientation and position imaging (FOPI) of AuNRs supported on a 50 nm thick gold film, which enables us to overcome the aforementioned limitations. Imaging AuNRs under the TIR scattering microscope provides excellent signal-to-noise ratio and results in no deteriorating images. The scattering patterns of AuNRs on the gold substrate are affected by the strong interaction of the excited dipole in the AuNR with the image dipole in the gold substrate. The doughnut-shaped scattering field distribution allows for high-throughput determination of the three-dimensional spatial orientation of in-focus AuNRs within a single frame without angular degeneracy. Therefore, the TIR scattering-based FOPI method is demonstrated to be an outstanding candidate for studying dynamics of functionalized nanoparticles on a large variety of functional surfaces.
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Affiliation(s)
- Ji Won Ha
- Ames Laboratory, U.S. Department of Energy, and Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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27
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Xiao L, Ha JW, Wei L, Wang G, Fang N. Determining the Full Three-Dimensional Orientation of Single Anisotropic Nanoparticles by Differential Interference Contrast Microscopy. Angew Chem Int Ed Engl 2012; 51:7734-8. [DOI: 10.1002/anie.201202340] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 04/30/2012] [Indexed: 01/09/2023]
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28
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Xiao L, Ha JW, Wei L, Wang G, Fang N. Determining the Full Three-Dimensional Orientation of Single Anisotropic Nanoparticles by Differential Interference Contrast Microscopy. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Lewis JH, Beausang JF, Sweeney HL, Goldman YE. The azimuthal path of myosin V and its dependence on lever-arm length. ACTA ACUST UNITED AC 2012; 139:101-20. [PMID: 22291144 PMCID: PMC3269788 DOI: 10.1085/jgp.201110715] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Myosin V (myoV) is a two-headed myosin capable of taking many successive steps along actin per diffusional encounter, enabling it to transport vesicular and ribonucleoprotein cargos in the dense and complex environment within cells. To better understand how myoV navigates along actin, we used polarized total internal reflection fluorescence microscopy to examine angular changes of bifunctional rhodamine probes on the lever arms of single myoV molecules in vitro. With a newly developed analysis technique, the rotational motions of the lever arm and the local orientation of each probe relative to the lever arm were estimated from the probe’s measured orientation. This type of analysis could be applied to similar studies on other motor proteins, as well as other proteins with domains that undergo significant rotational motions. The experiments were performed on recombinant constructs of myoV that had either the native-length (six IQ motifs and calmodulins [CaMs]) or truncated (four IQ motifs and CaMs) lever arms. Native-length myoV-6IQ mainly took straight steps along actin, with occasional small azimuthal tilts around the actin filament. Truncated myoV-4IQ showed an increased frequency of azimuthal steps, but the magnitudes of these steps were nearly identical to those of myoV-6IQ. The results show that the azimuthal deflections of myoV on actin are more common for the truncated lever arm, but the range of these deflections is relatively independent of its lever-arm length.
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Affiliation(s)
- John H Lewis
- The Pennsylvania Muscle Institute and Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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30
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Beausang JF, Sun Y, Quinlan ME, Forkey JN, Goldman YE. Orientation and rotational motions of single molecules by polarized total internal reflection fluorescence microscopy (polTIRFM). Cold Spring Harb Protoc 2012; 2012:2012/5/pdb.top069344. [PMID: 22550303 DOI: 10.1101/pdb.top069344] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this article, we describe methods to detect the spatial orientation and rotational dynamics of single molecules using polarized total internal reflection fluorescence microscopy (polTIRFM). polTIRFM determines the three-dimensional angular orientation and the extent of wobble of a fluorescent probe bound to the macromolecule of interest. We discuss single-molecule versus ensemble measurements, as well as single-molecule techniques for orientation and rotation, and fluorescent probes for orientation studies. Using calmodulin (CaM) as an example of a target protein, we describe a method for labeling CaM with bifunctional rhodamine (BR). We also describe the physical principles and experimental setup of polTIRFM. We conclude with a brief introduction to assays using polTIRFM to assess the interaction of actin and myosin.
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31
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Blum C, Schleifenbaum F, Stopel M, Peter S, Sackrow M, Subramaniam V, Meixner AJ. Room temperature excitation spectroscopy of single quantum dots. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2011; 2:516-24. [PMID: 22003458 PMCID: PMC3190622 DOI: 10.3762/bjnano.2.56] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 06/09/2011] [Indexed: 05/23/2023]
Abstract
We report a single molecule detection scheme to investigate excitation spectra of single emitters at room temperature. We demonstrate the potential of single emitter photoluminescence excitation spectroscopy by recording excitation spectra of single CdSe nanocrystals over a wide spectral range of 100 nm. The spectra exhibit emission intermittency, characteristic of single emitters. We observe large variations in the spectra close to the band edge, which represent the individual heterogeneity of the observed quantum dots. We also find specific excitation wavelengths for which the single quantum dots analyzed show an increased propensity for a transition to a long-lived dark state. We expect that the additional capability of recording excitation spectra at room temperature from single emitters will enable insights into the photophysics of emitters that so far have remained inaccessible.
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Affiliation(s)
- Christian Blum
- Nanobiophysics Group and MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Frank Schleifenbaum
- Center for Plant Molecular Biology, Biophysical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Martijn Stopel
- Nanobiophysics Group and MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Sébastien Peter
- Center for Plant Molecular Biology, Biophysical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Marcus Sackrow
- Institut für Physikalische und Theoretische Chemie, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- present address: Picoquant GmbH, Rudower Chaussee 29, 12489 Berlin, Germany
| | - Vinod Subramaniam
- Nanobiophysics Group and MESA+ Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
| | - Alfred J Meixner
- Institut für Physikalische und Theoretische Chemie, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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32
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Traub MC, Lakhwani G, Bolinger JC, Bout DV, Barbara PF. Electronic Energy Transfer in Highly Aligned MEH-PPV Single Chains. J Phys Chem B 2011; 115:9941-7. [DOI: 10.1021/jp204591p] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew C. Traub
- Center for Nano and Molecular Science and Technology and §Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, United States
| | - Girish Lakhwani
- Center for Nano and Molecular Science and Technology and §Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, United States
| | - Joshua C. Bolinger
- Center for Nano and Molecular Science and Technology and §Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, United States
| | - David Vanden Bout
- Center for Nano and Molecular Science and Technology and §Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, United States
| | - Paul F. Barbara
- Center for Nano and Molecular Science and Technology and §Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, United States
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33
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Xiao L, Qiao Y, He Y, Yeung ES. Imaging Translational and Rotational Diffusion of Single Anisotropic Nanoparticles with Planar Illumination Microscopy. J Am Chem Soc 2011; 133:10638-45. [DOI: 10.1021/ja203289m] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lehui Xiao
- College of Chemistry and Chemical Engineering, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
| | - Yanxia Qiao
- College of Chemistry and Chemical Engineering, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
| | - Yan He
- College of Chemistry and Chemical Engineering, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
| | - Edward S. Yeung
- College of Chemistry and Chemical Engineering, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, P. R. China
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34
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Ha JW, Sun W, Wang G, Fang N. Differential interference contrast polarization anisotropy for tracking rotational dynamics of gold nanorods. Chem Commun (Camb) 2011; 47:7743-5. [PMID: 21647523 DOI: 10.1039/c1cc11679g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe differential interference contrast (DIC) polarization anisotropy for tracking rotational dynamics of gold nanorod (AuNR) probes. DIC polarization anisotropy enabled us to reveal the unidirectional clockwise circular translocation of an AuNR attached to a kinesin-driven microtubule and to precisely determine the real-time orientation of the AuNR during the dynamic process.
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Affiliation(s)
- Ji Won Ha
- Ames Laboratory, U.S. Department of Energy, and Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
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35
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Abstract
The experimental study of individual macromolecules has opened a door to determining the details of their mechanochemical operation. Motor enzymes such as the myosin family have been particularly attractive targets for such study, in part because some of them are highly processive and their "product" is spatial motion. But single-molecule resolution comes with its own costs and limitations. Often, the observations rest on single fluorescent dye molecules, which emit a limited number of photons before photobleaching and are subject to complex internal dynamics. Thus, it is important to develop methods that extract the maximum useful information from a finite set of detected photons. We have extended an experimental technique, multiple polarization illumination in total internal reflection fluorescence microscopy (polTIRF), to record the arrival time and polarization state of each individual detected photon. We also extended an analysis technique, previously applied to FRET experiments, that optimally determines times of changes in photon emission rates. Combining these improvements allows us to identify the structural dynamics of a molecular motor (myosin V) with unprecedented detail and temporal resolution.
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36
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Reznik C, Berg R, Foster E, Advincula R, Landes CF. Transient 3-Dimensional Orientation of Molecular Ions in an Ordered Polyelectrolyte Membrane. J Phys Chem Lett 2011; 2:10.1021/jz200065f. [PMID: 24371507 PMCID: PMC3871193 DOI: 10.1021/jz200065f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Single-molecule fluorescence spectroscopy is employed to reveal 3-dimensional details of the mechanisms underpinning ion transport in a polyelectrolyte thin film possessing polymer-brush nanoscale order. The ability to resolve fluorescence emission over three discrete polarization angles reveals that these ordered materials impart 3-dimensional orientation to charged, diffusing molecules. The experiments, supported by simulations, report global orientation parameters for molecular transport, track dipole angle progressions over time, and identify a unique transport mechanism: translational diffusion with restricted rotation. Generally, realization of this experimental method for translational diffusion in systems exhibiting basic orientation should lend itself to evaluation of transport in a variety of important, ordered, functional materials.
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Affiliation(s)
| | | | - Ed Foster
- University of Houston, Houston, Texas 77204
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37
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Lu HP. Revealing time bunching effect in single-molecule enzyme conformational dynamics. Phys Chem Chem Phys 2011; 13:6734-49. [PMID: 21409227 DOI: 10.1039/c0cp02860f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we focus our discussion on how the single-molecule spectroscopy and statistical analysis are able to reveal enzyme hidden properties, taking the study of T4 lysozyme as an example. Protein conformational fluctuations and dynamics play a crucial role in biomolecular functions, such as in enzymatic reactions. Single-molecule spectroscopy is a powerful approach to analyze protein conformational dynamics under physiological conditions, providing dynamic perspectives on a molecular-level understanding of protein structure-function mechanisms. Using single-molecule fluorescence spectroscopy, we have probed T4 lysozyme conformational motions under the hydrolysis reaction of a polysaccharide of E. coli B cell walls by monitoring the fluorescence resonant energy transfer (FRET) between a donor-acceptor probe pair tethered to T4 lysozyme domains involving open-close hinge-bending motions. Based on the single-molecule spectroscopic results, molecular dynamics simulation, a random walk model analysis, and a novel 2D statistical correlation analysis, we have revealed a time bunching effect in protein conformational motion dynamics that is critical to enzymatic functions. Bunching effect implies that conformational motion times tend to bunch in a finite and narrow time window. We show that convoluted multiple Poisson rate processes give rise to the bunching effect in the enzymatic reaction dynamics. Evidently, the bunching effect is likely common in protein conformational dynamics involving in conformation-gated protein functions. In this perspective, we will also discuss a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anti-correlated fluctuations under a non-correlated noise background. Using this new method, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anti-correlated, or non-correlated; after which, a cross correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis.
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Affiliation(s)
- H Peter Lu
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, OH 43403, USA.
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38
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Structure and dynamics of the kinesin-microtubule interaction revealed by fluorescence polarization microscopy. Methods Cell Biol 2010. [PMID: 20466150 DOI: 10.1016/s0091-679x(10)95025-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
Fluorescence polarization microscopy (FPM) is the analysis of the polarization of light in a fluorescent microscope in order to determine the angular orientation and rotational mobility of fluorescent molecules. Key advantages of FPM, relative to other structural analysis techniques, are that it allows the detection of conformational changes of fluorescently labeled macromolecules in real time in physiological conditions and at the single-molecule level. In this chapter we describe in detail the FPM experimental set-up and analysis methods we have used to investigate structural intermediates of the motor protein kinesin-1 associated with its walking mechanism along microtubules. We also briefly describe additional FPM methods that have been used to investigate other macromolecular complexes.
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39
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Thomsson D, Lin H, Scheblykin IG. Correlation analysis of fluorescence intensity and fluorescence anisotropy fluctuations in single-molecule spectroscopy of conjugated polymers. Chemphyschem 2010; 11:897-904. [PMID: 20087921 DOI: 10.1002/cphc.200900724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single-molecule spectroscopy techniques are used to investigate time fluctuations of the fluorescence properties of two different types of conjugated polymer, a polythiophene derivative (PDOPT) and a phenylene vinylene derivative (MEH-PPV), at 100 and 293 K. Linear correlation coefficients between fluorescence intensity and polarization are used to characterize fluctuations. We are able to distinguish between different blinking and bleaching effects on the polarization. Furthermore, the polarization data reveal clear differences in the topology of these two polymers, which is related to the ordered conformation of the MEH-PPV. Plots of correlation coefficients appear to be very different for the two polymers and are also very sensitive to temperature. These observations prove that correlation analysis is a useful tool to understand fluorescence fluctuations in multi-chromophoric systems.
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Affiliation(s)
- Daniel Thomsson
- Department of Chemical Physics, Lund University, P.O. Box 124, 22100 Lund, Sweden
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40
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Single-molecule stepping and structural dynamics of myosin X. Nat Struct Mol Biol 2010; 17:485-91. [PMID: 20364131 DOI: 10.1038/nsmb.1785] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 02/03/2010] [Indexed: 11/08/2022]
Abstract
Myosin X is an unconventional myosin with puzzling motility properties. We studied the motility of dimerized myosin X using the single-molecule fluorescence techniques polTIRF, FIONA and Parallax to measure the rotation angles and three-dimensional position of the molecule during its walk. It was found that Myosin X steps processively in a hand-over-hand manner following a left-handed helical path along both single actin filaments and bundles. Its step size and velocity are smaller on actin bundles than individual filaments, suggesting myosin X often steps onto neighboring filaments in a bundle. The data suggest that a previously postulated single alpha-helical domain mechanically extends the lever arm, which has three IQ motifs, and either the neck-tail hinge or the tail is flexible. These structural features, in conjunction with the membrane- and microtubule-binding domains, enable myosin X to perform multiple functions on varied actin structures in cells.
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41
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Tani T, Sakai H, Usukura E, Suzuki T, Oda M. Single molecule and single quantum dot photodynamics by polarization-rotating modulation microscopy. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.phpro.2010.01.228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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42
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Abstract
Nanoparticles are actively exploited as biological imaging probes. Of particular interest are gold nanoparticles because of their nonblinking and nonbleaching absorption and scattering properties that arise from the excitation of surface plasmons. Nanoparticles with anisotropic shapes furthermore provide information about the probe orientation and its environment. Here we show how the orientation of single gold nanorods (25 x 73 nm) can be determined from both the transverse and longitudinal surface plasmon resonance by using polarization-sensitive photothermal imaging. By measuring the orientation of the same nanorods separately using scanning electron microscopy, we verified the high accuracy of this plasmon-absorption-based technique. However, care had to be taken when exciting the transverse plasmon absorption using a large numerical aperture objective as out-of-plane plasmon oscillations were also excited then. For the size regime studied here, being able to establish the nanorod orientation from the transverse mode is unique to photothermal imaging and almost impossible with conventional dark-field scattering spectroscopy. This is important because the transverse surface plasmon resonance is mostly insensitive to the medium refractive index and nanorod aspect ratio allowing nanorods of any length to be used as orientation sensors without changing the laser frequency.
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43
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Greene EC, Wind S, Fazio T, Gorman J, Visnapuu ML. DNA curtains for high-throughput single-molecule optical imaging. Methods Enzymol 2010; 472:293-315. [PMID: 20580969 DOI: 10.1016/s0076-6879(10)72006-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Single-molecule approaches provide a valuable tool in the arsenal of the modern biologist, and new discoveries continue to be made possible through the use of these state-of-the-art technologies. However, it can be inherently difficult to obtain statistically relevant data from experimental approaches specifically designed to probe individual reactions. This problem is compounded with more complex biochemical reactions, heterogeneous systems, and/or reactions requiring the use of long DNA substrates. Here we give an overview of a technology developed in our laboratory, which relies upon simple micro- or nanofabricated structures in combination with "bio-friendly" lipid bilayers, to align thousands of long DNA molecules into defined patterns on the surface of a microfluidic sample chamber. We call these "DNA curtains," and we have developed several different versions varying in complexity and DNA substrate configuration, which are designed to meet different experimental needs. This novel approach to single-molecule imaging provides a powerful experimental platform that offers the potential for concurrent observation of hundreds or even thousands of protein-DNA interactions in real time.
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Affiliation(s)
- Eric C Greene
- Howard Hughes Medical Institute, Columbia University, New York, NY, USA
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44
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Reznik C, Estillore N, Advincula RC, Landes CF. Single Molecule Spectroscopy Reveals Heterogeneous Transport Mechanisms for Molecular Ions in a Polyelectrolyte Polymer Brush. J Phys Chem B 2009; 113:14611-8. [DOI: 10.1021/jp906487j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carmen Reznik
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003
| | - Nicel Estillore
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003
| | | | - Christy F. Landes
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003
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45
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Ivanov V, Li M, Mizuuchi K. Impact of emission anisotropy on fluorescence spectroscopy and FRET distance measurements. Biophys J 2009; 97:922-9. [PMID: 19651051 PMCID: PMC2718156 DOI: 10.1016/j.bpj.2009.05.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 05/13/2009] [Accepted: 05/20/2009] [Indexed: 11/22/2022] Open
Abstract
The objective of this report is to provide a practical and improved method for estimating Förster resonance energy transfer distance measurement error due to unknown angles in the dipole orientation factor based on emission anisotropy measurements. We improve on the method of Dale et al. (1979), which has minor mistakes and is frequently interpreted in overly optimistic ways in the literature. To facilitate proper fluorescence intensity measurements, we also evaluated instrument parameters that could impact the measurement. The apparent fluorescence intensity of isotropic samples depends on the sample emission anisotropy, fluorometer geometry, and optical apertures. We separate parameters of the sample, and those of the cylindrically symmetric illumination source and detector in the equations describing results of unpolarized and polarized fluorescence intensity measurements. This approach greatly simplifies calculations compared with the more universal method of Axelrod (1989). We provide a full computational method for calculating the Förster resonance energy transfer distance error and present a graph describing distance error in the simplest case.
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Affiliation(s)
- Vassili Ivanov
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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46
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Hwang W, Lang MJ. Mechanical design of translocating motor proteins. Cell Biochem Biophys 2009; 54:11-22. [PMID: 19452133 DOI: 10.1007/s12013-009-9049-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 04/29/2009] [Indexed: 01/10/2023]
Abstract
Translocating motors generate force and move along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo transport, protein degradation, and muscle contraction. Advances in single molecule manipulation experiments, structural biology, and computational analysis are making it possible to consider common mechanical design principles of these diverse families of motors. Here, we propose a mechanical parts list that include track, energy conversion machinery, and moving parts. Energy is supplied not just by burning of a fuel molecule, but there are other sources or sinks of free energy, by binding and release of a fuel or products, or similarly between the motor and the track. Dynamic conformational changes of the motor domain can be regarded as controlling the flow of free energy to and from the surrounding heat reservoir. Multiple motor domains are organized in distinct ways to achieve motility under imposed physical constraints. Transcending amino acid sequence and structure, physically and functionally similar mechanical parts may have evolved as nature's design strategy for these molecular engines.
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Affiliation(s)
- Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA.
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47
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Oreopoulos J, Yip CM. Probing membrane order and topography in supported lipid bilayers by combined polarized total internal reflection fluorescence-atomic force microscopy. Biophys J 2009; 96:1970-84. [PMID: 19254557 DOI: 10.1016/j.bpj.2008.11.041] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 11/17/2008] [Indexed: 11/19/2022] Open
Abstract
Determining the local structure, dynamics, and conformational requirements for protein-protein and protein-lipid interactions in membranes is critical to understanding biological processes ranging from signaling to the translocating and membranolytic action of antimicrobial peptides. We report here the application of a combined polarized total internal reflection fluorescence microscopy-in situ atomic force microscopy platform. This platform's ability to image membrane orientational order was demonstrated on DOPC/DSPC/cholesterol model membranes containing the fluorescent membrane probe, DiI-C(20) or BODIPY-PC. Spatially resolved order parameters and fluorophore tilt angles extracted from the polarized total internal reflection fluorescence microscopy images were in good agreement with the topographical details resolved by in situ atomic force microscopy, portending use of this technique for high-resolution characterization of membrane domain structures and peptide-membrane interactions.
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Affiliation(s)
- John Oreopoulos
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
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48
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Khatua S, Guerrero JM, Claytor K, Vives G, Kolomeisky AB, Tour JM, Link S. Micrometer-scale translation and monitoring of individual nanocars on glass. ACS NANO 2009; 3:351-6. [PMID: 19236071 DOI: 10.1021/nn800798a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nanomachines designed to exhibit controlled mechanical motions on the molecular scale present new possibilities of building novel functional materials. Single molecule fluorescence imaging of dye-labeled nanocars on a glass surface at room temperature showed a coupled translational and rotational motion of these nanoscale machines with an activation energy of 42 +/- 5 kJ/mol. The 3 nm-long dye-labeled carborane-wheeled nanocars moved by as much as 2.5 mum with an average speed of 4.1 nm/s. Translation of the nanocars due a wheel-like rolling mechanism is proposed and this is consistent with the absence of movement for a three-wheeled nanocar analogue and the stationary behavior of unbound dye molecules. These findings are an important first step toward the rational design and ultimate control of surface-operational molecular machines.
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Affiliation(s)
- Saumyakanti Khatua
- Department of Chemistry and the Smalley Institute for Nanoscale Science and Technology, Rice University, 6100 Main Street, Houston, Texas 77005, USA
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49
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Tcherniak A, Reznik C, Link S, Landes CF. Fluorescence correlation spectroscopy: criteria for analysis in complex systems. Anal Chem 2009; 81:746-54. [PMID: 19093758 DOI: 10.1021/ac8013109] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have evaluated the effect of varying three key parameters for Fluorescence Correlation Spectroscopy analysis, first in the context of a one species/one environment system, and then in a complex system composed of two species, or conversely, two environments. We establish experimentally appropriate settings for the (1) minimum lag time, (2) maximum lag time, and (3) averaging times over which an autocorrelation is carried out, as a function of expected diffusion decay time for a particular solute, and show that use of appropriate settings plays a critical role in recovering accurate and reliable decay times and resulting diffusion constants. Both experimental and simulated data were used to show that for a complex binary system, to extract accurate diffusion constants for both species, decay times must be bounded by adequate minimum and maximum lag times as dictated by the fast and slow diffusing species, respectively. We also demonstrate that even when constraints on experimental conditions do not permit achieving the necessary lag time limits for both of the species in a binary system, the accuracy of the recovered diffusion constant for the one species whose autocorrelation function is fully time-resolved is unaffected by uncertainty in fitting introduced by the presence of the second species.
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Affiliation(s)
- Alexei Tcherniak
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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50
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Webb SED, Rolfe DJ, Needham SR, Roberts SK, Clarke DT, McLachlan CI, Hobson MP, Martin-Fernandez ML. Simultaneous widefield single molecule orientation and FRET microscopy in cells. OPTICS EXPRESS 2008; 16:20258-20265. [PMID: 19065164 DOI: 10.1364/oe.16.020258] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We combine single molecule fluorescence orientation imaging with single-pair fluorescence resonance energy transfer microscopy, using a total internal reflection microscope. We show how angles and FRET efficiencies can be determined for membrane proteins at the single molecule level and provide data from the epidermal growth factor receptor system in cells.
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Affiliation(s)
- S E D Webb
- Science and Technology Facilities Council, Daresbury Laboratory, Warrington WA4 4AD, UK.
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