1
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Dean WF, Nawara TJ, Albert RM, Mattheyses AL. OOPS: Object-Oriented Polarization Software for analysis of fluorescence polarization microscopy images. PLoS Comput Biol 2024; 20:e1011723. [PMID: 39133751 PMCID: PMC11341096 DOI: 10.1371/journal.pcbi.1011723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 08/22/2024] [Accepted: 08/02/2024] [Indexed: 08/24/2024] Open
Abstract
Most essential cellular functions are performed by proteins assembled into larger complexes. Fluorescence Polarization Microscopy (FPM) is a powerful technique that goes beyond traditional imaging methods by allowing researchers to measure not only the localization of proteins within cells, but also their orientation or alignment within complexes or cellular structures. FPM can be easily integrated into standard widefield microscopes with the addition of a polarization modulator. However, the extensive image processing and analysis required to interpret the data have limited its widespread adoption. To overcome these challenges and enhance accessibility, we introduce OOPS (Object-Oriented Polarization Software), a MATLAB package for object-based analysis of FPM data. By combining flexible image segmentation and novel object-based analyses with a high-throughput FPM processing pipeline, OOPS empowers researchers to simultaneously study molecular order and orientation in individual biological structures; conduct population assessments based on morphological features, intensity statistics, and FPM measurements; and create publication-quality visualizations, all within a user-friendly graphical interface. Here, we demonstrate the power and versatility of our approach by applying OOPS to punctate and filamentous structures.
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Affiliation(s)
- William F. Dean
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tomasz J. Nawara
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rose M. Albert
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Alexa L. Mattheyses
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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2
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Zhou W, Wu T, Lew MD. Fundamental Limits in Measuring the Anisotropic Rotational Diffusion of Single Molecules. J Phys Chem A 2024; 128:5808-5815. [PMID: 38978460 PMCID: PMC11298152 DOI: 10.1021/acs.jpca.4c03160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Many biophysical techniques, such as single-molecule fluorescence correlation spectroscopy, Förster resonance energy transfer, and fluorescence anisotropy, measure the translation and rotation of biomolecules to quantify molecular processes at the nanoscale. These methods often simplify data analysis by assuming isotropic rotational diffusion, e.g., that molecules wobble within a circular cone. This simplification ignores the anisotropy present in many biological contexts that may cause molecules to exhibit different degrees of diffusion in different directions. Here, we loosen this assumption and establish a theoretical framework for describing and measuring anisotropic rotational diffusion using fluorescence imaging. We show that anisotropic wobble is directly quantified by the eigenvalues of a 3-by-3 positive-semidefinite Hermitian matrix M consisting of the second-order moments of a molecule's transition dipole μ. This formalism enables us to model the influence of unavoidable shot noise using a Hermitian perturbation matrix E; the eigenvalues of E directly bound errors in measurements of wobble via Weyl's inequality. Quantifying various perturbations E reveals that anisotropic wobble measurements are generally more sensitive to errors compared to quantifying isotropic wobble. Moreover, severe shot noise can induce negative eigenvalues in estimates of M, thereby causing the anisotropic wobble measurement to fail. Our analysis, using Fisher information, shows that techniques with worse orientation measurement sensitivity experience stronger perturbations E and require larger signal to background ratios to measure anisotropic rotational diffusion accurately. Our work provides deep insights for improving the state of the art in imaging the orientations and anisotropic rotational diffusion of single molecules.
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Affiliation(s)
- Weiyan Zhou
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tingting Wu
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew D Lew
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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3
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Sun B, Ding T, Zhou W, Porter TS, Lew MD. Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay. NANO LETTERS 2024. [PMID: 38828968 DOI: 10.1021/acs.nanolett.4c01263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Amyloid-beta (Aβ42) aggregates are characteristic Alzheimer's disease signatures, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to Aβ42 fibrils. We correlate fibril architectures measured by SMOLM with their growth and decay over the course of 5 to 20 min visualized by single-molecule localization microscopy (SMLM). We discover that stable Aβ42 fibrils tend to be well-ordered and signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve β-sheet organization. SMOLM reveals that increased fibril architectural heterogeneity is correlated with dynamic remodeling and that large-scale fibril remodeling tends to originate from strongly heterogeneous local regions.
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Affiliation(s)
- Brian Sun
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tianben Ding
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Weiyan Zhou
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tara S Porter
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew D Lew
- Preston M. Green Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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4
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Steves MA, He C, Xu K. Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. Annu Rev Phys Chem 2024; 75:163-183. [PMID: 38360526 DOI: 10.1146/annurev-physchem-070623-034225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.
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Affiliation(s)
- Megan A Steves
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Changdong He
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California, USA;
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5
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Sun B, Ding T, Zhou W, Porter TS, Lew MD. Single-Molecule Orientation Imaging Reveals the Nano-Architecture of Amyloid Fibrils Undergoing Growth and Decay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.586510. [PMID: 38585908 PMCID: PMC10996564 DOI: 10.1101/2024.03.24.586510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Amyloid-beta ( A β 42 ) aggregates are characteristic signatures of Alzheimer's disease, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational "wobble" of Nile blue (NB) molecules transiently binding to A β 42 fibrils. We quantify correlations between fibril architectures, measured by SMOLM, and their growth and decay visualized by single-molecule localization microscopy (SMLM). We discover that stable A β 42 fibrils tend to be well-ordered, signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order and disorder are signatures of growing and decaying A β 42 fibrils, respectively. We also observe SMLM-invisible fibril remodeling, including steady growth and decay patterns that conserve β -sheet organization. SMOLM reveals that increased heterogeneity in fibril architectures is correlated with more dynamic remodeling and that large-scale fibril remodeling tends to originate from local regions that exhibit strong heterogeneity.
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Affiliation(s)
- Brian Sun
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Tianben Ding
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Weiyan Zhou
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Tara S. Porter
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130
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6
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the Nanoscale Structure of β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation-Localization Microscopy. ACS NANO 2024; 18:8798-8810. [PMID: 38478911 PMCID: PMC11025465 DOI: 10.1021/acsnano.3c11771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize by using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8L and KFE8D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) ribbon structure of both KFE8 and Aβ42 and quantifies the precise tilt of the fibrils' inner and outer backbones in relevant buffer conditions without the need for covalent labeling or sequence mutations. SMOLM also distinguishes polymorphic branched and curved morphologies of KFE8, whose backbones exhibit much more heterogeneity than those of typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross-β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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7
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Chandler T, Guo M, Su Y, Chen J, Wu Y, Liu J, Agashe A, Fischer RS, Mehta SB, Kumar A, Baskin TI, Jamouillé V, Liu H, Swaminathan V, Nain A, Oldenbourg R, Riviére PL, Shroff H. Three-dimensional spatio-angular fluorescence microscopy with a polarized dual-view inverted selective-plane illumination microscope (pol-diSPIM). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.09.584243. [PMID: 38712306 PMCID: PMC11071302 DOI: 10.1101/2024.03.09.584243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Polarized fluorescence microscopy is a valuable tool for measuring molecular orientations, but techniques for recovering three-dimensional orientations and positions of fluorescent ensembles are limited. We report a polarized dual-view light-sheet system for determining the three-dimensional orientations and diffraction-limited positions of ensembles of fluorescent dipoles that label biological structures, and we share a set of visualization, histogram, and profiling tools for interpreting these positions and orientations. We model our samples, their excitation, and their detection using coarse-grained representations we call orientation distribution functions (ODFs). We apply ODFs to create physics-informed models of image formation with spatio-angular point-spread and transfer functions. We use theory and experiment to conclude that light-sheet tilting is a necessary part of our design for recovering all three-dimensional orientations. We use our system to extend known two-dimensional results to three dimensions in FM1-43-labelled giant unilamellar vesicles, fast-scarlet-labelled cellulose in xylem cells, and phalloidin-labelled actin in U2OS cells. Additionally, we observe phalloidin-labelled actin in mouse fibroblasts grown on grids of labelled nanowires and identify correlations between local actin alignment and global cell-scale orientation, indicating cellular coordination across length scales.
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Affiliation(s)
- Talon Chandler
- CZ Biohub SF, San Francisco, 94158, California, USA
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA
| | - Min Guo
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, 20147, Virginia, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Junyu Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Atharva Agashe
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, 24061, Virginia, USA
| | - Robert S. Fischer
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA
| | - Shalin B. Mehta
- CZ Biohub SF, San Francisco, 94158, California, USA
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA
- Bell Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Abhishek Kumar
- Bell Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Tobias I. Baskin
- Biology Department, University of Massachusetts, Amherst, 01003, Maryland, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Valentin Jamouillé
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, V5A 1S6, British Columbia, Canada
| | - Huafeng Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Vinay Swaminathan
- Department of Clinical Sciences, Lund University, Lund, SE-221 00, Scania, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, SE-221 00, Scania, Sweden
| | - Amrinder Nain
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, 24061, Virginia, USA
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, 24061, Virginia, USA
| | - Rudolf Oldenbourg
- Bell Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Patrick La Riviére
- Department of Radiology, University of Chicago, Chicago, 60637, Illinois, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, 20892, Maryland, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, 20147, Virginia, USA
- Whitman Center, Marine Biological Laboratory, Woods Hole, 02543, Massachusetts, USA
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8
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Wu T, King MR, Farag M, Pappu RV, Lew MD. Single fluorogen imaging reveals distinct environmental and structural features of biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525727. [PMID: 36747818 PMCID: PMC9900924 DOI: 10.1101/2023.01.26.525727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Recent computations suggest that biomolecular condensates that form via macromolecular phase separation are network fluids featuring spatially inhomogeneous organization of the underlying molecules. Computations also point to unique conformations of molecules at condensate interfaces. Here, we test these predictions using high-resolution structural characterizations of condensates formed by intrinsically disordered prion-like low complexity domains (PLCDs). We leveraged the localization and orientational preferences of freely diffusing fluorogens and the solvatochromic effect whereby specific fluorogens are turned on in response to the physic-chemical properties of condensate microenvironments to facilitate single-molecule tracking and super-resolution imaging. We deployed three different fluorogens to probe internal microenvironments and molecular organization of PLCD condensates. The spatiotemporal resolution and environmental sensitivity afforded by single-fluorogen imaging shows that the internal environments of condensates are more hydrophobic than coexisting dilute phases. Molecules within condensates are organized in a spatially inhomogeneous manner featuring slow-moving nanoscale molecular clusters or hubs that coexist with fast-moving molecules. Finally, molecules at interfaces of condensates are found to have distinct orientational preferences when compared to the interiors. Our findings, which affirm computational predictions, help provide a structural basis for condensate viscoelasticity and dispel the notion of protein condensates being isotropic liquids defined by uniform internal densities.
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Affiliation(s)
- Tingting Wu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Matthew R King
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Mina Farag
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
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9
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Shen M, Rackers WH, Sadtler B. Getting the Most Out of Fluorogenic Probes: Challenges and Opportunities in Using Single-Molecule Fluorescence to Image Electro- and Photocatalysis. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:692-715. [PMID: 38037609 PMCID: PMC10685636 DOI: 10.1021/cbmi.3c00075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 12/02/2023]
Abstract
Single-molecule fluorescence microscopy enables the direct observation of individual reaction events at the surface of a catalyst. It has become a powerful tool to image in real time both intra- and interparticle heterogeneity among different nanoscale catalyst particles. Single-molecule fluorescence microscopy of heterogeneous catalysts relies on the detection of chemically activated fluorogenic probes that are converted from a nonfluorescent state into a highly fluorescent state through a reaction mediated at the catalyst surface. This review article describes challenges and opportunities in using such fluorogenic probes as proxies to develop structure-activity relationships in nanoscale electrocatalysts and photocatalysts. We compare single-molecule fluorescence microscopy to other microscopies for imaging catalysis in situ to highlight the distinct advantages and limitations of this technique. We describe correlative imaging between super-resolution activity maps obtained from multiple fluorogenic probes to understand the chemical origins behind spatial variations in activity that are frequently observed for nanoscale catalysts. Fluorogenic probes, originally developed for biological imaging, are introduced that can detect products such as carbon monoxide, nitrite, and ammonia, which are generated by electro- and photocatalysts for fuel production and environmental remediation. We conclude by describing how single-molecule imaging can provide mechanistic insights for a broader scope of catalytic systems, such as single-atom catalysts.
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Affiliation(s)
- Meikun Shen
- Department
of Chemistry and Biochemistry, University
of Oregon, Eugene, Oregon 97403, United States
| | - William H. Rackers
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Bryce Sadtler
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
- Institute
of Materials Science & Engineering, Washington University, St. Louis, Missouri 63130, United States
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10
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Zhou W, O’Neill CL, Ding T, Zhang O, Rudra JS, Lew MD. Resolving the nanoscale structure of β-sheet assemblies using single-molecule orientation-localization microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557571. [PMID: 37745382 PMCID: PMC10515885 DOI: 10.1101/2023.09.13.557571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Synthetic peptides that self-assemble into cross-β fibrils have remarkable utility as engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarity to amyloid species has been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers, KFE8L and KFE8D, and the pathological amyloid-beta peptide Aβ42. SMOLM reveals that the orientations of Nile red, as it transiently binds to both KFE8 and Aβ42, are consistent with a helical (bilayer) ribbon structure and convey the precise tilt of the fibrils' inner and outer backbones. SMOLM also finds polymorphic branched and curved morphologies of KFE8 whose backbones exhibit much more heterogeneity than those of more typical straight fibrils. Thus, SMOLM is a powerful tool to interrogate the structural differences and polymorphism between engineered and pathological cross β-rich fibrils.
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Affiliation(s)
- Weiyan Zhou
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Conor L. O’Neill
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Jai S. Rudra
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, McKelvey School of Engineering, Washington University in St. Louis, MO 63130, USA
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11
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Liu Y, Shahid MA, Mao H, Chen J, Waddington M, Song KH, Zhang Y. Switchable and Functional Fluorophores for Multidimensional Single-Molecule Localization Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:403-413. [PMID: 37655169 PMCID: PMC10466381 DOI: 10.1021/cbmi.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 09/02/2023]
Abstract
Multidimensional single-molecule localization microscopy (mSMLM) represents a paradigm shift in the realm of super-resolution microscopy techniques. It affords the simultaneous detection of single-molecule spatial locations at the nanoscale and functional information by interrogating the emission properties of switchable fluorophores. The latter is finely tuned to report its local environment through carefully manipulated laser illumination and single-molecule detection strategies. This Perspective highlights recent strides in mSMLM with a focus on fluorophore designs and their integration into mSMLM imaging systems. Particular interests are the accomplishments in simultaneous multiplexed super-resolution imaging, nanoscale polarity and hydrophobicity mapping, and single-molecule orientational imaging. Challenges and prospects in mSMLM are also discussed, which include the development of more vibrant and functional fluorescent probes, the optimization of optical implementation to judiciously utilize the photon budget, and the advancement of imaging analysis and machine learning techniques.
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Affiliation(s)
- Yunshu Liu
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Md Abul Shahid
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Hongjing Mao
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Jiahui Chen
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Michael Waddington
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Ki-Hee Song
- Quantum
Optics Research Division, Korea Atomic Energy
Research Institute, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Yang Zhang
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
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12
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Sarkar A, Namboodiri V, Kumbhakar M. Single-Molecule Orientation Imaging Reveals Two Distinct Binding Configurations on Amyloid Fibrils. J Phys Chem Lett 2023:4990-4996. [PMID: 37220418 DOI: 10.1021/acs.jpclett.3c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Fluorescence readouts for an amyloid fibril sensor critically depend on its molecular interaction and local environment offered by the available structural motifs. Here we employ polarized points accumulation for imaging in nanoscale topography with intramolecular charge transfer probes transiently bound to amyloid fibrils to investigate the organization of fibril nanostructures and probe binding configurations. Besides the in-plane (θ ≈ 90°) mode for binding on the fibril surface parallel to the long fibril axis, we also observed a sizable population of over 60% out-of-plane (θ < 60°) dipoles for rotor probes experiencing a varying degree of orientational mobility. Highly confined dipoles exhibiting an out-of-plane configuration probably reflect tightly bound dipoles in the inner channel grooves, while the weakly bound ones on amyloid enjoy rotational flexibility. Our observation of an out-of-plane binding mode emphasizes the pivotal role played by the electron donor amino group toward fluorescence detection and hence the emergence of anchored probes alongside conventional groove binders.
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Affiliation(s)
- Aranyak Sarkar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinu Namboodiri
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Center, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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13
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Steves M, Knappenberger KL. Distinguishing Single-Metal Nanoparticles with Subdiffraction Spatial Resolution Using Variable-Polarization Fourier Transform Nonlinear Optical Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:91-98. [PMID: 37122832 PMCID: PMC10131489 DOI: 10.1021/cbmi.3c00008] [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: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 05/02/2023]
Abstract
The development and use of interferometric variable-polarization Fourier transform nonlinear optical (vpFT-NLO) imaging to distinguish colloidal nanoparticles colocated within the optical diffraction limit is described. Using a collinear train of phase-stabilized pulse pairs with orthogonal electric field vectors, the polarization of nonlinear excitation fields are controllably modulated between linear, circular, and various elliptical states. Polarization modulation is achieved by precise control over the time delay separating the orthogonal pulse pairs to within hundreds of attoseconds. The resultant emission from gold nanorods is imaged to a 2D array detector and correlated to the excitation field polarization and plasmon resonance frequency by Fourier transformation. Gold nanorods with length-to-diameter aspect ratios of 2 support a longitudinal surface plasmon resonance at approximately 800 nm, which is resonant with the excitation fundamental carrier wavelength. Differences in the intrinsic linear and circular dichroism resulting from variation in their relative alignment with respect to the laboratory frame enable optical differentiation of nanorods separated within 50 nm, which is an approximate 5-fold improvement over the diffraction limit of the microscope. The experimental results are supported by analytical simulations. In addition to subdiffraction spatial resolution, the vpFT-NLO method intrinsically provides the polarization- and frequency-dependent resonance response of the nanoparticles-providing spectroscopic information content along with super-resolution imaging capabilities.
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Affiliation(s)
| | - Kenneth L. Knappenberger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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14
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Sun Y, Jack K, Ercolani T, Sangar D, Hosszu L, Collinge J, Bieschke J. Direct Observation of Competing Prion Protein Fibril Populations with Distinct Structures and Kinetics. ACS NANO 2023; 17:6575-6588. [PMID: 36802500 PMCID: PMC10100569 DOI: 10.1021/acsnano.2c12009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In prion diseases, fibrillar assemblies of misfolded prion protein (PrP) self-propagate by incorporating PrP monomers. These assemblies can evolve to adapt to changing environments and hosts, but the mechanism of prion evolution is poorly understood. We show that PrP fibrils exist as a population of competing conformers, which are selectively amplified under different conditions and can "mutate" during elongation. Prion replication therefore possesses the steps necessary for molecular evolution analogous to the quasispecies concept of genetic organisms. We monitored structure and growth of single PrP fibrils by total internal reflection and transient amyloid binding super-resolution microscopy and detected at least two main fibril populations, which emerged from seemingly homogeneous PrP seeds. All PrP fibrils elongated in a preferred direction by an intermittent "stop-and-go" mechanism, but each population possessed distinct elongation mechanisms that incorporated either unfolded or partially folded monomers. Elongation of RML and ME7 prion rods likewise exhibited distinct kinetic features. The discovery of polymorphic fibril populations growing in competition, which were previously hidden in ensemble measurements, suggests that prions and other amyloid replicating by prion-like mechanisms may represent quasispecies of structural isomorphs that can evolve to adapt to new hosts and conceivably could evade therapeutic intervention.
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Affiliation(s)
- Yuanzi Sun
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Kezia Jack
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Tiziana Ercolani
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Daljit Sangar
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Laszlo Hosszu
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - John Collinge
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Jan Bieschke
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
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15
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Zhang O, Guo Z, He Y, Wu T, Vahey MD, Lew MD. Six-Dimensional Single-Molecule Imaging with Isotropic Resolution using a Multi-View Reflector Microscope. NATURE PHOTONICS 2023; 17:179-186. [PMID: 36968242 PMCID: PMC10035538 DOI: 10.1038/s41566-022-01116-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/20/2022] [Indexed: 05/31/2023]
Abstract
Imaging both the positions and orientations of single fluorophores, termed single-molecule orientation-localisation microscopy, is a powerful tool to study biochemical processes. However, the limited photon budget associated with single-molecule fluorescence makes high-dimensional imaging with isotropic, nanoscale spatial resolution a formidable challenge. Here, we realise a radially and azimuthally polarized multi-view reflector (raMVR) microscope for the imaging of the 3D positions and 3D orientations of single molecules, with precision of 10.9 nm and 2.0° over a 1.5 μm depth range. The raMVR microscope achieves 6D super-resolution imaging of Nile red (NR) molecules transiently bound to lipid-coated spheres, accurately resolving their spherical morphology despite refractive-index mismatch. By observing the rotational dynamics of NR, raMVR images also resolve the infiltration of lipid membranes by amyloid-beta oligomers without covalent labelling. Finally, we demonstrate 6D imaging of cell membranes, where the orientations of specific fluorophores reveal heterogeneity in membrane fluidity. With its nearly isotropic 3D spatial resolution and orientation measurement precision, we expect the raMVR microscope to enable 6D imaging of molecular dynamics within biological and chemical systems with exceptional detail.
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Affiliation(s)
- Oumeng Zhang
- Department of Electrical and Systems Engineering
| | | | | | - Tingting Wu
- Department of Electrical and Systems Engineering
| | - Michael D. Vahey
- Department of Biomedical Engineering
- Center for Biomolecular Condensates
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering
- Center for Biomolecular Condensates
- Institute of Materials Science and Engineering, Washington University in St. Louis, Missouri 63130, USA
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16
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Brasselet S. Unraveling the geometry of complex protein organizations by polarized fluorescence imaging. Biophys J 2022; 121:4242-4243. [PMID: 36182666 PMCID: PMC9702980 DOI: 10.1016/j.bpj.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Sophie Brasselet
- Aix Marseille University, CNRS, Centrale Marseille, Institut Fresnel, Marseille, France.
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17
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Brasselet S. Fluorescence polarization modulation super-resolution imaging provides refined dynamics orientation processes in biological samples. LIGHT, SCIENCE & APPLICATIONS 2022; 11:322. [PMID: 36336677 PMCID: PMC9637731 DOI: 10.1038/s41377-022-01018-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Combining polarization modulation Fourier analysis and spatial information in a joint reconstruction algorithm for polarization-resolved fluorescence imaging provides not only a gain in spatial resolution but also a sensitive readout of anisotropy in cell samples.
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Affiliation(s)
- Sophie Brasselet
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France.
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18
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Wu T, Lu P, Rahman MA, Li X, Lew MD. Deep-SMOLM: deep learning resolves the 3D orientations and 2D positions of overlapping single molecules with optimal nanoscale resolution. OPTICS EXPRESS 2022; 30:36761-36773. [PMID: 36258598 PMCID: PMC9662599 DOI: 10.1364/oe.470146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 06/01/2023]
Abstract
Dipole-spread function (DSF) engineering reshapes the images of a microscope to maximize the sensitivity of measuring the 3D orientations of dipole-like emitters. However, severe Poisson shot noise, overlapping images, and simultaneously fitting high-dimensional information-both orientation and position-greatly complicates image analysis in single-molecule orientation-localization microscopy (SMOLM). Here, we report a deep-learning based estimator, termed Deep-SMOLM, that achieves superior 3D orientation and 2D position measurement precision within 3% of the theoretical limit (3.8° orientation, 0.32 sr wobble angle, and 8.5 nm lateral position using 1000 detected photons). Deep-SMOLM also demonstrates state-of-art estimation performance on overlapping images of emitters, e.g., a 0.95 Jaccard index for emitters separated by 139 nm, corresponding to a 43% image overlap. Deep-SMOLM accurately and precisely reconstructs 5D information of both simulated biological fibers and experimental amyloid fibrils from images containing highly overlapped DSFs at a speed ~10 times faster than iterative estimators.
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Affiliation(s)
- Tingting Wu
- Department of Electrical and Systems Engineering,
Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems,
Washington University in St. Louis, Missouri 63130, USA
| | - Peng Lu
- Department of Biomedical Engineering, Washington University in St. Louis, Missouri 63130, USA
- Department of Radiology, Washington University School of Medicine, Missouri 63110, USA
- These authors contributed equally to this work
| | - Md Ashequr Rahman
- Department of Biomedical Engineering, Washington University in St. Louis, Missouri 63130, USA
- Department of Radiology, Washington University School of Medicine, Missouri 63110, USA
- These authors contributed equally to this work
| | - Xiao Li
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, USA
- These authors contributed equally to this work
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering,
Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems,
Washington University in St. Louis, Missouri 63130, USA
- Institute of Materials Science and Engineering,
Washington University in St. Louis, Missouri 63130, USA
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19
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Wu T, Lu J, Lew MD. Dipole-spread-function engineering for simultaneously measuring the 3D orientations and 3D positions of fluorescent molecules. OPTICA 2022; 9:505-511. [PMID: 35601691 PMCID: PMC9122034 DOI: 10.1364/optica.451899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/03/2022] [Indexed: 06/01/2023]
Abstract
Interactions between biomolecules are characterized by both where they occur and how they are organized, e.g., the alignment of lipid molecules to form a membrane. However, spatial and angular information are mixed within the image of a fluorescent molecule-the microscope's dipole-spread function (DSF). We demonstrate the pixOL algorithm for simultaneously optimizing all pixels within a phase mask to produce an engineered Green's tensor-the dipole extension of point-spread function engineering. The pixOL DSF achieves optimal precision for measuring simultaneously the 3D orientation and 3D location of a single molecule, i.e., 4.1° orientation, 0.44 sr wobble angle, 23.2 nm lateral localization, and 19.5 nm axial localization precisions in simulations over a 700-nm depth range using 2500 detected photons. The pixOL microscope accurately and precisely resolves the 3D positions and 3D orientations of Nile red within a spherical supported lipid bilayer, resolving both membrane defects and differences in cholesterol concentration in 6 dimensions.
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Affiliation(s)
- Tingting Wu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, Missouri 63130, USA
| | - Jin Lu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, Missouri 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, Missouri 63130, USA
- Institute of Materials Science and Engineering, Washington University in St. Louis, Missouri 63130, USA
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20
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Thorsen RØ, Hulleman CN, Rieger B, Stallinga S. Photon efficient orientation estimation using polarization modulation in single-molecule localization microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:2835-2858. [PMID: 35774337 PMCID: PMC9203119 DOI: 10.1364/boe.452159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 06/01/2023]
Abstract
Combining orientation estimation with localization microscopy opens up the possibility to analyze the underlying orientation of biomolecules on the nanometer scale. Inspired by the recent improvement of the localization precision by shifting excitation patterns (MINFLUX, SIMFLUX), we have adapted the idea towards the modulation of excitation polarization to enhance the orientation precision. For this modality two modes are analyzed: i) normally incident excitation with three polarization steps to retrieve the in-plane angle of emitters and ii) obliquely incident excitation with p-polarization with five different azimuthal angles of incidence to retrieve the full orientation. Firstly, we present a theoretical study of the lower precision limit with a Cramér-Rao bound for these modes. For the oblique incidence mode we find a favorable isotropic orientation precision for all molecular orientations if the polar angle of incidence is equal to arccos 2 / 3 ≈ 35 degrees. Secondly, a simulation study is performed to assess the performance for low signal-to-background ratios and how inaccurate illumination polarization angles affect the outcome. We show that a precision, at the Cramér-Rao bound (CRB) limit, of just 2.4 and 1.6 degrees in the azimuthal and polar angles can be achieved with only 1000 detected signal photons and 10 background photons per pixel (about twice better than reported earlier). Lastly, the alignment and calibration of an optical microscope with polarization control is described in detail. With this microscope a proof-of-principle experiment is carried out, demonstrating an experimental in-plane precision close to the CRB limit for signal photon counts ranging from 400 to 10,000.
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Affiliation(s)
- Rasmus Ø Thorsen
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
| | - Christiaan N Hulleman
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
- These authors contributed equally
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21
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Zhang O, Zhou W, Lu J, Wu T, Lew MD. Resolving the Three-Dimensional Rotational and Translational Dynamics of Single Molecules Using Radially and Azimuthally Polarized Fluorescence. NANO LETTERS 2022; 22:1024-1031. [PMID: 35073487 PMCID: PMC8893020 DOI: 10.1021/acs.nanolett.1c03948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR's orientational diffusion to be dramatically reduced, but curiously NR's median lateral displacements drastically increase from 20.8 to 75.5 nm (200 ms time lag). These jump diffusion events overwhelmingly originate from cholesterol-rich nanodomains within the SLB. These detailed measurements of single-molecule rotational and translational dynamics are made possible by raPol's high measurement precision and are not detectable in standard SMLM.
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22
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Rimoli CV, Valades-Cruz CA, Curcio V, Mavrakis M, Brasselet S. 4polar-STORM polarized super-resolution imaging of actin filament organization in cells. Nat Commun 2022; 13:301. [PMID: 35027553 PMCID: PMC8758668 DOI: 10.1038/s41467-022-27966-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022] Open
Abstract
Single-molecule localization microscopy provides insights into the nanometer-scale spatial organization of proteins in cells, however it does not provide information on their conformation and orientation, which are key functional signatures. Detecting single molecules' orientation in addition to their localization in cells is still a challenging task, in particular in dense cell samples. Here, we present a polarization-splitting scheme which combines Stochastic Optical Reconstruction Microscopy (STORM) with single molecule 2D orientation and wobbling measurements, without requiring a strong deformation of the imaged point spread function. This method called 4polar-STORM allows, thanks to a control of its detection numerical aperture, to determine both single molecules' localization and orientation in 2D and to infer their 3D orientation. 4polar-STORM is compatible with relatively high densities of diffraction-limited spots in an image, and is thus ideally placed for the investigation of dense protein assemblies in cells. We demonstrate the potential of this method in dense actin filament organizations driving cell adhesion and motility.
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Affiliation(s)
- Caio Vaz Rimoli
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France
| | - Cesar Augusto Valades-Cruz
- Institut Curie, PSL Research University, UMR144 CNRS, Space-Time imaging of organelles and Endomembranes Dynamics Team, F-75005, Paris, France
- Inria Centre Rennes-Bretagne Atlantique, SERPICO Project Team, F-35042, Rennes, France
| | - Valentina Curcio
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France
| | - Manos Mavrakis
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France.
| | - Sophie Brasselet
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France.
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23
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Mahato J, Ray KK, Das S, Kadu P, Maji SK, Chowdhury A. Investigation of Structural Heterogeneity in Individual Amyloid Fibrils Using Polarization-Resolved Microscopy. J Phys Chem B 2021; 125:13406-13414. [PMID: 34861110 DOI: 10.1021/acs.jpcb.1c08604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid fibrils are structurally heterogeneous protein aggregates that are implicated in a wide range of neurodegenerative and other proteopathic diseases. These fibrils exist in a variety of different tertiary and higher-level structures, and this exhibited polymorphism greatly complicates any structural study of amyloid fibrils. In this work, we demonstrate a method of using polarization-resolved microscopy to directly observe the structural heterogeneity of individual amyloid fibrils using amyloid-bound fluorophores. We formulate a mathematical quantity, helical anisotropy, which utilizes the polarized emission of amyloid-bound fluorophores to report on the local structure of individual fibrils. Using this method, we show how model amyloid fibrils generated from short peptides exhibit diverse structural properties both between different fibrils and within a single fibril, in a manner that is replicated for fibrils assembled from longer proteins. Our method represents an accessible and easily adaptable technique by which polymorphism in the structure of amyloid fibrils can be probed. Additionally, the methodology we describe here can be easily extended to the study of other fibrillar and otherwise ordered supramolecular structures.
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Affiliation(s)
- Jaladhar Mahato
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Korak Kumar Ray
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Subhadeep Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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24
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Ding T, Lew MD. Single-Molecule Localization Microscopy of 3D Orientation and Anisotropic Wobble Using a Polarized Vortex Point Spread Function. J Phys Chem B 2021; 125:12718-12729. [PMID: 34766758 PMCID: PMC8662813 DOI: 10.1021/acs.jpcb.1c08073] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Within condensed matter, single fluorophores are sensitive probes of their chemical environments, but it is difficult to use their limited photon budget to image precisely their positions, 3D orientations, and rotational diffusion simultaneously. We demonstrate the polarized vortex point spread function (PSF) for measuring these parameters, including characterizing the anisotropy of a molecule's wobble, simultaneously from a single image. Even when imaging dim emitters (∼500 photons detected), the polarized vortex PSF can obtain 12 nm localization precision, 4°-8° orientation precision, and 26° wobble precision. We use the vortex PSF to measure the emission anisotropy of fluorescent beads, the wobble dynamics of Nile red (NR) within supported lipid bilayers, and the distinct orientation signatures of NR in contact with amyloid-beta fibrils, oligomers, and tangles. The unparalleled sensitivity of the vortex PSF transforms single-molecule microscopes into nanoscale orientation imaging spectrometers, where the orientations and wobbles of individual probes reveal structures and organization of soft matter that are nearly impossible to perceive by using molecular positions alone.
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Affiliation(s)
- Tianben Ding
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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25
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Hulleman CN, Thorsen RØ, Kim E, Dekker C, Stallinga S, Rieger B. Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. Nat Commun 2021; 12:5934. [PMID: 34635658 PMCID: PMC8505439 DOI: 10.1038/s41467-021-26228-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 09/21/2021] [Indexed: 11/08/2022] Open
Abstract
Estimating the orientation and 3D position of rotationally constrained emitters with localization microscopy typically requires polarization splitting or a large engineered Point Spread Function (PSF). Here we utilize a compact modified PSF for single molecule emitter imaging to estimate simultaneously the 3D position, dipole orientation, and degree of rotational constraint from a single 2D image. We use an affordable and commonly available phase plate, normally used for STED microscopy in the excitation light path, to alter the PSF in the emission light path. This resulting Vortex PSF does not require polarization splitting and has a compact PSF size, making it easy to implement and combine with localization microscopy techniques. In addition to a vectorial PSF fitting routine we calibrate for field-dependent aberrations which enables orientation and position estimation within 30% of the Cramér-Rao bound limit over a 66 μm field of view. We demonstrate this technique on reorienting single molecules adhered to the cover slip, λ-DNA with DNA intercalators using binding-activated localization microscopy, and we reveal periodicity on intertwined structures on supercoiled DNA.
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Affiliation(s)
- Christiaan N Hulleman
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Rasmus Ø Thorsen
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Max Planck Institute of Biophysics, 60438, Frankfurt, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
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26
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Chen CD, Joseph-Mathurin N, Sinha N, Zhou A, Li Y, Friedrichsen K, McCullough A, Franklin EE, Hornbeck R, Gordon B, Sharma V, Cruchaga C, Goate A, Karch C, McDade E, Xiong C, Bateman RJ, Ghetti B, Ringman JM, Chhatwal J, Masters CL, McLean C, Lashley T, Su Y, Koeppe R, Jack C, Klunk WE, Morris JC, Perrin RJ, Cairns NJ, Benzinger TLS. Comparing amyloid-β plaque burden with antemortem PiB PET in autosomal dominant and late-onset Alzheimer disease. Acta Neuropathol 2021; 142:689-706. [PMID: 34319442 PMCID: PMC8815340 DOI: 10.1007/s00401-021-02342-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
Pittsburgh compound B (PiB) radiotracer for positron emission tomography (PET) imaging can bind to different types of amyloid-β plaques and blood vessels (cerebral amyloid angiopathy). However, the relative contributions of different plaque subtypes (diffuse versus cored/compact) to in vivo PiB PET signal on a region-by-region basis are incompletely understood. Of particular interest is whether the same staging schemes for summarizing amyloid-β burden are appropriate for both late-onset and autosomal dominant forms of Alzheimer disease (LOAD and ADAD). Here, we compared antemortem PiB PET with follow-up postmortem estimation of amyloid-β burden using stereologic methods to estimate the relative area fraction of diffuse and cored/compact amyloid-β plaques across 16 brain regions in 15 individuals with ADAD and 14 individuals with LOAD. In ADAD, we found that PiB PET correlated with diffuse plaques in the frontal, parietal, temporal, and striatal regions commonly used to summarize amyloid-β burden in PiB PET, and correlated with both diffuse and cored/compact plaques in the occipital lobe and parahippocampal gyrus. In LOAD, we found that PiB PET correlated with both diffuse and cored/compact plaques in the anterior cingulate, frontal lobe (middle frontal gyrus), and parietal lobe, and showed additional correlations with diffuse plaque in the amygdala and occipital lobe, and with cored/compact plaque in the temporal lobe. Thus, commonly used PiB PET summary regions predominantly reflect diffuse plaque burden in ADAD and a mixture of diffuse and cored/compact plaque burden in LOAD. In direct comparisons of ADAD and LOAD, postmortem stereology identified much greater mean amyloid-β plaque burdens in ADAD versus LOAD across almost all brain regions studied. However, standard PiB PET did not recapitulate these stereologic findings, likely due to non-trivial amyloid-β plaque burdens in ADAD within the cerebellum and brainstem-commonly used reference regions in PiB PET. Our findings suggest that PiB PET summary regions correlate with amyloid-β plaque burden in both ADAD and LOAD; however, they might not be reliable in direct comparisons of regional amyloid-β plaque burden between the two forms of AD.
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Affiliation(s)
- Charles D Chen
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Nelly Joseph-Mathurin
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Namita Sinha
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Pathology, University of Manitoba, Shared Health, Winnipeg, MB, Canada
| | - Aihong Zhou
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yan Li
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Karl Friedrichsen
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Austin McCullough
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Erin E Franklin
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Russ Hornbeck
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Brian Gordon
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Vijay Sharma
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Alison Goate
- Department of Genetics and Genomic Sciences, Ichan School of Medicine at Mount Sinai, New York, NY, USA
| | - Celeste Karch
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Eric McDade
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Chengjie Xiong
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Randall J Bateman
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John M Ringman
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Jasmeer Chhatwal
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Catriona McLean
- Department of Anatomic Pathology, Alfred Hospital, Melbourne, VIC, Australia
| | - Tammaryn Lashley
- UCL Queen Square Institute of Neurology, University College London, London, UK
- Queen Square Brain Bank for Neurological Disorders, University College London, London, UK
| | - Yi Su
- Banner Alzheimer's Institute, Banner Health, Phoenix, AZ, USA
- Arizona Alzheimer's Consortium, Banner Health, Phoenix, AZ, USA
| | - Robert Koeppe
- Department of Radiology, University of Michigan, Ann Arbor, MI, USA
| | - Clifford Jack
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - William E Klunk
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - John C Morris
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Richard J Perrin
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Nigel J Cairns
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Tammie L S Benzinger
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, MO, USA.
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27
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Xiang L, Chen K, Xu K. Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. ACS NANO 2021; 15:12483-12496. [PMID: 34304562 PMCID: PMC8789943 DOI: 10.1021/acsnano.1c04708] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.
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28
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Lu M, Ward E, van Tartwijk FW, Kaminski CF. Advances in the study of organelle interactions and their role in neurodegenerative diseases enabled by super-resolution microscopy. Neurobiol Dis 2021; 159:105475. [PMID: 34390833 DOI: 10.1016/j.nbd.2021.105475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/28/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022] Open
Abstract
From the first illustrations of neuronal morphology by Ramón y Cajal to the recent three-dimensional reconstruction of synaptic connections, the development of modern neuroscience has greatly benefited from breakthroughs in imaging technology. This also applies specifically to the study of neurodegenerative diseases. Much of the research into these diseases relies on the direct visualisation of intracellular structures and their dynamics in degenerating neural cells, which cannot be fully resolved by diffraction-limited microscopes. Progress in the field has therefore been closely linked to the development of super-resolution imaging methods. Their application has greatly advanced our understanding of disease mechanisms, ranging from the structural progression of protein aggregates to defects in organelle morphology. Recent super-resolution studies have specifically implicated the disruption of inter-organelle interactions in multiple neurodegenerative diseases. In this article, we describe some of the key super-resolution techniques that have contributed to this field. We then discuss work to visualise changes in the structure and dynamics of organelles and associated dysfunctions. Finally, we consider what future developments in imaging technology may further our knowledge of these processes.
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Affiliation(s)
- Meng Lu
- Cambridge Infinitus Research Centre, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Edward Ward
- Cambridge Infinitus Research Centre, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Clemens F Kaminski
- Cambridge Infinitus Research Centre, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK; UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AH, UK.
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29
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Backer AS, King GA, Biebricher AS, Shepherd JW, Noy A, Leake MC, Heller I, Wuite GJL, Peterman EJG. Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy. J Phys Chem B 2021; 125:8351-8361. [PMID: 34309392 PMCID: PMC8350907 DOI: 10.1021/acs.jpcb.1c02708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/01/2021] [Indexed: 11/29/2022]
Abstract
The combination of DNA force spectroscopy and polarization microscopy of fluorescent DNA intercalator dyes can provide valuable insights into the structure of DNA under tension. These techniques have previously been used to characterize S-DNA-an elongated DNA conformation that forms when DNA overstretches at forces ≥ 65 pN. In this way, it was deduced that the base pairs of S-DNA are highly inclined, relative to those in relaxed (B-form) DNA. However, it is unclear whether and how topological constraints on the DNA may influence the base-pair inclinations under tension. Here, we apply polarization microscopy to investigate the impact of DNA pulling geometry, torsional constraint, and negative supercoiling on the orientations of intercalated dyes during overstretching. In contrast to earlier predictions, the pulling geometry (namely, whether the DNA molecule is stretched via opposite strands or the same strand) is found to have little influence. However, torsional constraint leads to a substantial reduction in intercalator tilting in overstretched DNA, particularly in AT-rich sequences. Surprisingly, the extent of intercalator tilting is similarly reduced when the DNA molecule is negatively supercoiled up to a critical supercoiling density (corresponding to ∼70% reduction in the linking number). We attribute these observations to the presence of P-DNA (an overwound DNA conformation). Our results suggest that intercalated DNA preferentially flanks regions of P-DNA rather than those of S-DNA and also substantiate previous suggestions that P-DNA forms predominantly in AT-rich sequences.
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Affiliation(s)
- Adam S. Backer
- Apple Inc, 1 Apple Park Way, Cupertino, California 95014, United States
| | - Graeme A. King
- Institute
of Structural and Molecular Biology, University
College London, Gower Street, London WC1E
6BT, U.K.
| | - Andreas S. Biebricher
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Jack W. Shepherd
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Agnes Noy
- Department
of Physics, University of York, York YO10 5DD, U.K.
| | - Mark C. Leake
- Department
of Physics, University of York, York YO10 5DD, U.K.
- Department
of Biology, University of York, York YO10 5DD, U.K.
| | - Iddo Heller
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Gijs J. L. Wuite
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Erwin J. G. Peterman
- Department
of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
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30
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Shepherd JW, Payne-Dwyer AL, Lee JE, Syeda A, Leake MC. Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes. JPHYS PHOTONICS 2021. [DOI: 10.1088/2515-7647/ac015d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Super-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization of proteins in cellular processes. These enable measurement of spatial location to a super-resolved precision better than the diffraction-limited optical resolution, as well as estimation of molecular stoichiometry based on the brightness of individual fluorophores. In this innovation we have adapted a millisecond timescale microscope used for single-molecule detection to enable splitting of fluorescence polarization emissions into two separate imaging channels for s- and p-polarization signals, which are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein, single combed DNA molecules, and protein assemblies and complexes from live Escherichia coli and Saccharomyces cerevisiae cells. Our findings are qualitative but demonstrate promise in showing how fluorescence polarization and super-resolved localization microscopy can be combined on the same sample to enable simultaneous measurements of polarization and stoichiometry of tracked molecular complexes, as well as the translational diffusion coefficient.
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31
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Zhang O, Lew MD. Single-molecule orientation localization microscopy II: a performance comparison. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2021; 38:288-297. [PMID: 33690542 DOI: 10.1364/josaa.411983] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Various techniques have been developed to measure the 2D and 3D positions and 2D and 3D orientations of fluorescent molecules with improved precision over standard epifluorescence microscopes. Due to the challenging signal-to-background ratio in typical single-molecule experiments, it is essential to choose an imaging system optimized for the specific target sample. In this work, we compare the performance of multiple state-of-the-art and commonly used methods for orientation localization microscopy against the fundamental limits of measurement precision. Our analysis reveals optimal imaging methods for various experiment conditions and sample geometries. Interestingly, simple modifications to the standard fluorescence microscope exhibit superior performance in many imaging scenarios.
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32
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Zhang O, Lew MD. Single-molecule orientation localization microscopy I: fundamental limits. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2021; 38:277-287. [PMID: 33690541 DOI: 10.1364/josaa.411981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
Precisely measuring the three-dimensional position and orientation of individual fluorophores is challenging due to the substantial photon shot noise in single-molecule experiments. Facing this limited photon budget, numerous techniques have been developed to encode 2D and 3D position and 2D and 3D orientation information into fluorescence images. In this work, we adapt classical and quantum estimation theory and propose a mathematical framework to derive the best possible precision for measuring the position and orientation of dipole-like emitters for any fixed imaging system. We find that it is impossible to design an instrument that achieves the maximum sensitivity limit for measuring all possible rotational motions. Further, our vectorial dipole imaging model shows that the best quantum-limited localization precision is 4%-8% worse than that suggested by a scalar monopole model. Overall, we conclude that no single instrument can be optimized for maximum precision across all possible 2D and 3D localization and orientation measurement tasks.
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33
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Mazidi H, Ding T, Nehorai A, Lew MD. Quantifying accuracy and heterogeneity in single-molecule super-resolution microscopy. Nat Commun 2020; 11:6353. [PMID: 33311471 PMCID: PMC7732856 DOI: 10.1038/s41467-020-20056-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 11/10/2020] [Indexed: 12/03/2022] Open
Abstract
The resolution and accuracy of single-molecule localization microscopes (SMLMs) are routinely benchmarked using simulated data, calibration rulers, or comparisons to secondary imaging modalities. However, these methods cannot quantify the nanoscale accuracy of an arbitrary SMLM dataset. Here, we show that by computing localization stability under a well-chosen perturbation with accurate knowledge of the imaging system, we can robustly measure the confidence of individual localizations without ground-truth knowledge of the sample. We demonstrate that our method, termed Wasserstein-induced flux (WIF), measures the accuracy of various reconstruction algorithms directly on experimental 2D and 3D data of microtubules and amyloid fibrils. We further show that WIF confidences can be used to evaluate the mismatch between computational models and imaging data, enhance the accuracy and resolution of reconstructed structures, and discover hidden molecular heterogeneities. As a computational methodology, WIF is broadly applicable to any SMLM dataset, imaging system, and localization algorithm. Standard benchmarking of single-molecule localization microscopy cannot quantify nanoscale accuracy of arbitrary datasets. Here, the authors present Wasserstein-induced flux, a method using a chosen perturbation and knowledge of the imaging system to measure confidence of individual localizations.
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Affiliation(s)
- Hesam Mazidi
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Arye Nehorai
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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34
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Abstract
Optical studies of single molecules have taught us much over the past three decades, but these individual quantum-mechanical objects continue to have promise as probes of nanoscale structure and dynamics in complex systems.
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Affiliation(s)
- W E Moerner
- Departments of Chemistry and of Applied Physics (courtesy), Stanford University, Stanford, California 94305-4401, United States
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35
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Möckl L, Moerner WE. Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. J Am Chem Soc 2020; 142:17828-17844. [PMID: 33034452 PMCID: PMC7582613 DOI: 10.1021/jacs.0c08178] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/31/2022]
Abstract
Single-molecule super-resolution microscopy has developed from a specialized technique into one of the most versatile and powerful imaging methods of the nanoscale over the past two decades. In this perspective, we provide a brief overview of the historical development of the field, the fundamental concepts, the methodology required to obtain maximum quantitative information, and the current state of the art. Then, we will discuss emerging perspectives and areas where innovation and further improvement are needed. Despite the tremendous progress, the full potential of single-molecule super-resolution microscopy is yet to be realized, which will be enabled by the research ahead of us.
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Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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36
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Curcio V, Alemán-Castañeda LA, Brown TG, Brasselet S, Alonso MA. Birefringent Fourier filtering for single molecule coordinate and height super-resolution imaging with dithering and orientation. Nat Commun 2020; 11:5307. [PMID: 33082309 PMCID: PMC7576605 DOI: 10.1038/s41467-020-19064-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 09/18/2020] [Indexed: 01/25/2023] Open
Abstract
Super-resolution imaging based on single molecule localization allows accessing nanometric-scale information in biological samples with high precision. However, complete measurements including molecule orientation are still challenging. Orientation is intrinsically coupled to position in microscopy imaging, and molecular wobbling during the image integration time can bias orientation measurements. Providing 3D molecular orientation and orientational fluctuations would offer new ways to assess the degree of alignment of protein structures, which cannot be monitored by pure localization. Here we demonstrate that by adding polarization control to phase control in the Fourier plane of the imaging path, all parameters can be determined unambiguously from single molecules: 3D spatial position, 3D orientation and wobbling or dithering angle. The method, applied to fluorescent labels attached to single actin filaments, provides precisions within tens of nanometers in position and few degrees in orientation. Determining the orientation of single molecules in super resolution imaging is challenging. Here, by adding polarization control to phase control in the Fourier plane of the imaging path, parameters such as 3D spatial position, 3D orientation and wobbling or dithering angle can be determined from single molecules.
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Affiliation(s)
- Valentina Curcio
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France
| | - Luis A Alemán-Castañeda
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France.,The Institute of Optics, University of Rochester, Rochester, NY, 14627, USA
| | - Thomas G Brown
- The Institute of Optics, University of Rochester, Rochester, NY, 14627, USA
| | - Sophie Brasselet
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France.
| | - Miguel A Alonso
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013, Marseille, France. .,The Institute of Optics, University of Rochester, Rochester, NY, 14627, USA.
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37
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Lu J, Mazidi H, Ding T, Zhang O, Lew MD. Single-Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes. Angew Chem Int Ed Engl 2020; 59:17572-17579. [PMID: 32648275 PMCID: PMC7794097 DOI: 10.1002/anie.202006207] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Indexed: 12/21/2022]
Abstract
In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm-2 ) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single-molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus "wobble") of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve nanodomains and enzyme-induced compositional heterogeneity within membranes, where NR within liquid-ordered vs. liquid-disordered domains shows a ≈4° difference in polar angle and a ≈0.3π sr difference in wobble angle. As a new type of imaging spectroscopy, SMOLM exposes the organizational and functional dynamics of lipid-lipid, lipid-protein, and lipid-dye interactions with single-molecule, nanoscale resolution.
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Affiliation(s)
- Jin Lu
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Hesam Mazidi
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Center for Science and Engineering of Living Systems, Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
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38
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Lu J, Mazidi H, Ding T, Zhang O, Lew MD. Single‐Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jin Lu
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Hesam Mazidi
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Oumeng Zhang
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering Center for Science and Engineering of Living Systems Institute of Materials Science and Engineering Washington University in St. Louis St. Louis MO 63130 USA
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39
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Zhang O, Lew MD. Quantum limits for precisely estimating the orientation and wobble of dipole emitters. PHYSICAL REVIEW RESEARCH 2020; 2:033114. [PMID: 32832916 PMCID: PMC7440618 DOI: 10.1103/physrevresearch.2.033114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Precisely measuring molecular orientation is key to understanding how molecules organize and interact in soft matter, but the maximum theoretical limit of measurement precision has yet to be quantified. We use quantum estimation theory and Fisher information (QFI) to derive a fundamental bound on the precision of estimating the orientations of rotationally fixed molecules. While direct imaging of the microscope pupil achieves the quantum bound, it is not compatible with wide-field imaging, so we propose an interferometric imaging system that also achieves QFI-limited measurement precision. Extending our analysis to rotationally diffusing molecules, we derive conditions that enable a subset of second-order dipole orientation moments to be measured with quantum-limited precision. Interestingly, we find that no existing techniques can measure all second moments simultaneously with QFI-limited precision; there exists a fundamental trade-off between precisely measuring the mean orientation of a molecule versus its wobble. This theoretical analysis provides crucial insight for optimizing the design of orientation-sensitive imaging systems.
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Affiliation(s)
- Oumeng Zhang
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
| | - Matthew D. Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, Missouri 63130, USA
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