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Yan X, Yu PY, Srinivasan A, Abdul Rehman S, Prigozhin MB. Identifying Intermolecular Interactions in Single-Molecule Localization Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593617. [PMID: 38798627 PMCID: PMC11118527 DOI: 10.1101/2024.05.10.593617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Intermolecular interactions underlie all cellular functions, yet visualizing these interactions at the single-molecule level remains challenging. Single-molecule localization microscopy (SMLM) offers a potential solution. Given a nanoscale map of two putative interaction partners, it should be possible to assign molecules either to the class of coupled pairs or to the class of non-coupled bystanders. Here, we developed a probabilistic algorithm that allows accurate determination of both the absolute number and the proportion of molecules that form coupled pairs. The algorithm calculates interaction probabilities for all possible pairs of localized molecules, selects the most likely interaction set, and corrects for any spurious colocalizations. Benchmarking this approach across a set of simulated molecular localization maps with varying densities (up to ∼ 50 molecules µm - 2 ) and localization precisions (5 to 50 nm) showed typical errors in the identification of correct pairs of only a few percent. At molecular densities of ∼ 5-10 molecules µm - 2 and localization precisions of 20-30 nm, which are typical parameters for SMLM imaging, the recall was ∼ 90%. The algorithm was effective at differentiating between non-interacting and coupled molecules both in simulations and experiments. Finally, it correctly inferred the number of coupled pairs over time in a simulated reaction-diffusion system, enabling determination of the underlying rate constants. The proposed approach promises to enable direct visualization and quantification of intermolecular interactions using SMLM.
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2
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Hernandez AC, Ortiz S, Betancur LI, Dojčilović R, Picco A, Kaksonen M, Oliva B, Gallego O. PyF2F: a robust and simplified fluorophore-to-fluorophore distance measurement tool for Protein interactions from Imaging Complexes after Translocation experiments. NAR Genom Bioinform 2024; 6:lqae027. [PMID: 38486885 PMCID: PMC10939353 DOI: 10.1093/nargab/lqae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/31/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Structural knowledge of protein assemblies in their physiological environment is paramount to understand cellular functions at the molecular level. Protein interactions from Imaging Complexes after Translocation (PICT) is a live-cell imaging technique for the structural characterization of macromolecular assemblies in living cells. PICT relies on the measurement of the separation between labelled molecules using fluorescence microscopy and cell engineering. Unfortunately, the required computational tools to extract molecular distances involve a variety of sophisticated software programs that challenge reproducibility and limit their implementation to highly specialized researchers. Here we introduce PyF2F, a Python-based software that provides a workflow for measuring molecular distances from PICT data, with minimal user programming expertise. We used a published dataset to validate PyF2F's performance.
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Affiliation(s)
- Altair C Hernandez
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005, Catalonia, Spain
| | - Sebastian Ortiz
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005, Catalonia, Spain
| | - Laura I Betancur
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005, Catalonia, Spain
| | - Radovan Dojčilović
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005, Catalonia, Spain
| | - Andrea Picco
- Department of Biochemistry, University of Geneva, 1205 Genève, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry, University of Geneva, 1205 Genève, Switzerland
| | - Baldo Oliva
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005, Catalonia, Spain
| | - Oriol Gallego
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona 08005, Catalonia, Spain
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3
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Schodt DJ, Cutler PJ, Becerra FE, Lidke KA. Tolerance to aberration and misalignment in a two-point-resolving image inversion interferometer. OPTICS EXPRESS 2023; 31:16393-16405. [PMID: 37157718 PMCID: PMC10316753 DOI: 10.1364/oe.487808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/19/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
Image inversion interferometry can measure the separation of two incoherent point sources at or near the quantum limit. This technique has the potential to improve upon current state-of-the-art imaging technologies, with applications ranging from microbiology to astronomy. However, unavoidable aberrations and imperfections in real systems may prevent inversion interferometry from providing an advantage for real-world applications. Here, we numerically study the effects of realistic imaging system imperfections on the performance of image inversion interferometry, including common phase aberrations, interferometer misalignment, and imperfect energy splitting within the interferometer. Our results suggest that image inversion interferometry retains its superiority to direct detection imaging for a wide range of aberrations, so long as pixelated detection is used at the interferometer outputs. This study serves as a guide for the system requirements needed to achieve sensitivities beyond the limits of direct imaging, and further elucidates the robustness of image inversion interferometry to imperfections. These results are critical for the design, construction, and use of future imaging technologies performing at or near the quantum limit of source separation measurements.
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Affiliation(s)
- David J. Schodt
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, USA
- Teledyne Scientific & Imaging, LLC, USA
| | | | - Francisco E. Becerra
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, USA
- Center for Quantum Information and Control, University of New Mexico, Albuquerque, New Mexico, USA
| | - Keith A. Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, USA
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4
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Embacher PA, Germanova TE, Roscioli E, McAinsh AD, Burroughs NJ. Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution. PLoS Comput Biol 2022; 18:e1010765. [PMID: 36574448 PMCID: PMC9829179 DOI: 10.1371/journal.pcbi.1010765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/09/2023] [Accepted: 11/28/2022] [Indexed: 12/29/2022] Open
Abstract
Gaussian spot fitting methods have significantly extended the spatial range where fluorescent microscopy can be used, with recent techniques approaching nanometre (nm) resolutions. However, small inter-fluorophore distances are systematically over-estimated for typical molecular scales. This bias can be corrected computationally, but current algorithms are limited to correcting distances between pairs of fluorophores. Here we present a flexible Bayesian computational approach that infers the distances and angles between multiple fluorophores and has several advantages over these previous methods. Specifically it improves confidence intervals for small lengths, estimates measurement errors of each fluorophore individually and infers the correlations between polygon lengths. The latter is essential for determining the full multi-fluorophore 3D architecture. We further developed the algorithm to infer the mixture composition of a heterogeneous population of multiple polygon states. We use our algorithm to analyse the 3D architecture of the human kinetochore, a macro-molecular complex that is essential for high fidelity chromosome segregation during cell division. Using triple fluorophore image data we unravel the mixture of kinetochore states during human mitosis, inferring the conformation of microtubule attached and unattached kinetochores and their proportions across mitosis. We demonstrate that the attachment conformation correlates with intersister tension and sister alignment to the metaphase plate.
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Affiliation(s)
- Peter A. Embacher
- Department of Medical Physics & Biomedical Engineering, University College London, London, United Kingdom
| | - Tsvetelina E. Germanova
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Emanuele Roscioli
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Andrew D. McAinsh
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Nigel J. Burroughs
- Mathematics Institute and Zeeman Institute, University of Warwick, Coventry, United Kingdom
- * E-mail:
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5
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Jonsson E, Htet ZM, Bard JA, Dong KC, Martin A. Ubiquitin modulates 26 S proteasome conformational dynamics and promotes substrate degradation. SCIENCE ADVANCES 2022; 8:eadd9520. [PMID: 36563145 PMCID: PMC9788759 DOI: 10.1126/sciadv.add9520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
The 26S proteasome recognizes thousands of appropriate protein substrates in eukaryotic cells through attached ubiquitin chains and uses its adenosine triphosphatase (ATPase) motor for mechanical unfolding and translocation into a proteolytic chamber. Here, we used single-molecule Förster resonance energy transfer measurements to monitor the conformational dynamics of the proteasome, observe individual substrates during their progression toward degradation, and elucidate how these processes are regulated by ubiquitin chains. Rapid transitions between engagement- and processing-competent proteasome conformations control substrate access to the ATPase motor. Ubiquitin chain binding functions as an allosteric regulator to slow these transitions, stabilize the engagement-competent state, and aid substrate capture to accelerate degradation initiation. Upon substrate engagement, the proteasome remains in processing-competent states for translocation and unfolding, except for apparent motor slips when encountering stably folded domains. Our studies revealed how ubiquitin chains allosterically regulate degradation initiation, which ensures substrate selectivity in a crowded cellular environment.
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Affiliation(s)
- Erik Jonsson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | | | - Ken C. Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
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6
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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7
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Extraction of accurate cytoskeletal actin velocity distributions from noisy measurements. Nat Commun 2022; 13:4749. [PMID: 35963858 PMCID: PMC9376101 DOI: 10.1038/s41467-022-31583-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
Dynamic remodeling of the actin cytoskeleton is essential for many cellular processes. Tracking the movement of individual actin filaments can in principle shed light on how this complex behavior arises at the molecular level. However, the information that can be extracted from these measurements is often limited by low signal-to-noise ratios. We developed a Bayesian statistical approach to estimate true, underlying velocity distributions from the tracks of individual actin-associated fluorophores with quantified localization uncertainties. We found that the motion of filamentous (F)-actin in fibroblasts and endothelial cells was better described by a statistical jump process than by models in which filaments undergo continuous, diffusive movement. In particular, a model with exponentially distributed jump length- and time-scales recapitulated actin filament velocity distributions measured for the cell cortex, integrin-based adhesions, and stress fibers, suggesting that a common physical model can potentially describe actin filament dynamics in a variety of cellular contexts.
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8
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Shaw TR, Fazekas FJ, Kim S, Flanagan-Natoli JC, Sumrall ER, Veatch SL. Estimating the localization spread function of static single-molecule localization microscopy images. Biophys J 2022; 121:2906-2920. [PMID: 35787472 PMCID: PMC9388596 DOI: 10.1016/j.bpj.2022.06.036] [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: 03/04/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 11/27/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) permits the visualization of cellular structures an order of magnitude smaller than the diffraction limit of visible light, and an accurate, objective evaluation of the resolution of an SMLM data set is an essential aspect of the image processing and analysis pipeline. Here, we present a simple method to estimate the localization spread function (LSF) of a static SMLM data set directly from acquired localizations, exploiting the correlated dynamics of individual emitters and properties of the pair autocorrelation function evaluated in both time and space. The method is demonstrated on simulated localizations, DNA origami rulers, and cellular structures labeled by dye-conjugated antibodies, DNA-PAINT, or fluorescent fusion proteins. We show that experimentally obtained images have LSFs that are broader than expected from the localization precision alone, due to additional uncertainty accrued when localizing molecules imaged over time.
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Affiliation(s)
- Thomas R Shaw
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan; Program in Applied Physics, University of Michigan, Ann Arbor, Michigan
| | - Frank J Fazekas
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Sumin Kim
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan
| | | | - Emily R Sumrall
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan; Program in Applied Physics, University of Michigan, Ann Arbor, Michigan.
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9
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Three-color single-molecule imaging reveals conformational dynamics of dynein undergoing motility. Proc Natl Acad Sci U S A 2021; 118:2101391118. [PMID: 34326255 PMCID: PMC8346880 DOI: 10.1073/pnas.2101391118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Dynein, a dimeric motor protein, moves along microtubules through adenosine 5′-triphosphate- and thermal-driven motions of two large ring domains (AAA rings) and small microtubule-binding domains (MTBDs) separated by a long coiled-coil. Previous single-molecule studies have tracked the positions of the AAA rings during motility, but not the MTBDs. Here, we tracked the relative positions of both MTBDs and one AAA ring by three-color, nanometer-resolution imaging. The observation of both MTBDs provided a direct measurement of how dynein steps on the tubulin subunits, and the simultaneous observation of three fiducial markers revealed extraordinary flexibility and previously unknown conformational states of the motor during motility. The techniques presented here can be used to explore conformational dynamics of many other macromolecular complexes. The motor protein dynein undergoes coordinated conformational changes of its domains during motility along microtubules. Previous single-molecule studies analyzed the motion of the AAA rings of the dynein homodimer, but not the distal microtubule-binding domains (MTBDs) that step along the track. Here, we simultaneously tracked with nanometer precision two MTBDs and one AAA ring of a single dynein as it underwent hundreds of steps using three-color imaging. We show that the AAA ring and the MTBDs do not always step simultaneously and can take differently sized steps. This variability in the movement between the AAA ring and MTBDs results in an unexpectedly large number of conformational states of dynein during motility. Extracting data on conformational transition biases, we could accurately model dynein stepping in silico. Our results reveal that the flexibility between major dynein domains is critical for dynein motility.
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10
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You S, Chao J, Cohen EAK, Ward ES, Ober RJ. Microscope calibration protocol for single-molecule microscopy. OPTICS EXPRESS 2021; 29:182-207. [PMID: 33362108 PMCID: PMC7920521 DOI: 10.1364/oe.408361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Single-molecule microscopy allows for the investigation of the dynamics of individual molecules and the visualization of subcellular structures at high spatial resolution. For single-molecule imaging experiments, and particularly those that entail the acquisition of multicolor data, calibration of the microscope and its optical components therefore needs to be carried out at a high level of accuracy. We propose here a method for calibrating a microscope at the nanometer scale, in the sense of determining optical aberrations as revealed by point source localization errors on the order of nanometers. The method is based on the imaging of a standard sample to detect and evaluate the amount of geometric aberration introduced in the optical light path. To provide support for multicolor imaging, it also includes procedures for evaluating the geometric aberration caused by a dichroic filter and the axial chromatic aberration introduced by an objective lens.
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Affiliation(s)
- Sungyong You
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Jerry Chao
- Astero Technologies LLC, College Station, TX 77845, USA
| | | | - E. Sally Ward
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Raimund J. Ober
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, TX 77843, USA
- Centre for Cancer Immunology, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
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11
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Taguchi Y, Saio T, Kohda D. Distance Distribution between Two Iodine Atoms Derived from Small-Angle X-ray Scattering Interferometry for Analyzing a Conformational Ensemble of Heavy Atom-Labeled Small Molecules. J Phys Chem Lett 2020; 11:5451-5456. [PMID: 32558579 DOI: 10.1021/acs.jpclett.0c01107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
To obtain unbiased information about the dynamic conformational ensemble of a molecule in solution, one promising approach is small-angle X-ray scattering (SAXS). Conventionally, SAXS data are converted to a pair distribution function, which describes the distance distribution between all pairs of atoms within a molecule. If two strong X-ray scatterers are introduced and the background contributions from the other atoms are suppressed, then the distance distribution between the two scatterers provides spatial information about a flexible molecule. Gold nanocrystals can provide such information for distances of >50 Å. Here, we synthesized a chemical compound containing two iodine atoms attached to the ends of a flexible polyethylene glycol chain and used the relevant singly labeled and unlabeled compounds to suppress the background contribution. This is a feasibility demonstration to prove that the distance distribution in the range of 10-30 Å can be experimentally accessed by SAXS.
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Affiliation(s)
- Yuya Taguchi
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tomohide Saio
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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12
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Son S, Takatori SC, Belardi B, Podolski M, Bakalar MH, Fletcher DA. Molecular height measurement by cell surface optical profilometry (CSOP). Proc Natl Acad Sci U S A 2020; 117:14209-14219. [PMID: 32513731 PMCID: PMC7322024 DOI: 10.1073/pnas.1922626117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The physical dimensions of proteins and glycans on cell surfaces can critically affect cell function, for example, by preventing close contact between cells and limiting receptor accessibility. However, high-resolution measurements of molecular heights on native cell membranes have been difficult to obtain. Here we present a simple and rapid method that achieves nanometer height resolution by localizing fluorophores at the tip and base of cell surface molecules and determining their separation by radially averaging across many molecules. We use this method, which we call cell surface optical profilometry (CSOP), to quantify the height of key multidomain proteins on a model cell, as well as to capture average protein and glycan heights on native cell membranes. We show that average height of a protein is significantly smaller than its contour length, due to thermally driven bending and rotation on the membrane, and that height strongly depends on local surface and solution conditions. We find that average height increases with cell surface molecular crowding but decreases with solution crowding by solutes, both of which we confirm with molecular dynamics simulations. We also use experiments and simulations to determine the height of an epitope, based on the location of an antibody, which allows CSOP to profile various proteins and glycans on a native cell surface using antibodies and lectins. This versatile method for profiling cell surfaces has the potential to advance understanding of the molecular landscape of cells and the role of the molecular landscape in cell function.
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Affiliation(s)
- Sungmin Son
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Sho C Takatori
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Brian Belardi
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Marija Podolski
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Matthew H Bakalar
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720
| | - Daniel A Fletcher
- Department of Bioengineering and Biophysics Program, University of California, Berkeley, CA 94720;
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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13
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Coelho S, Baek J, Graus MS, Halstead JM, Nicovich PR, Feher K, Gandhi H, Gooding JJ, Gaus K. Ultraprecise single-molecule localization microscopy enables in situ distance measurements in intact cells. SCIENCE ADVANCES 2020; 6:eaay8271. [PMID: 32494604 PMCID: PMC7164934 DOI: 10.1126/sciadv.aay8271] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/23/2020] [Indexed: 05/24/2023]
Abstract
Single-molecule localization microscopy (SMLM) has the potential to quantify the diversity in spatial arrangements of molecules in intact cells. However, this requires that the single-molecule emitters are localized with ultrahigh precision irrespective of the sample format and the length of the data acquisition. We advance SMLM to enable direct distance measurements between molecules in intact cells on the scale between 1 and 20 nm. Our actively stabilized microscope combines three-dimensional real-time drift corrections and achieves a stabilization of <1 nm and localization precision of ~1 nm. To demonstrate the biological applicability of the new microscope, we show a 4- to 7-nm difference in spatial separations between signaling T cell receptors and phosphatases (CD45) in active and resting T cells. In summary, by overcoming the major bottlenecks in SMLM imaging, it is possible to generate molecular images with nanometer accuracy and conduct distance measurements on the biological relevant length scales.
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Affiliation(s)
- Simao Coelho
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, New South Wales, Australia
| | - Jongho Baek
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew S. Graus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, New South Wales, Australia
| | - James M. Halstead
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Kristen Feher
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, New South Wales, Australia
| | - Hetvi Gandhi
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, New South Wales, Australia
| | - J. Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, New South Wales, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, New South Wales, Australia
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14
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A 6-nm ultra-photostable DNA FluoroCube for fluorescence imaging. Nat Methods 2020; 17:437-441. [PMID: 32203385 PMCID: PMC7138518 DOI: 10.1038/s41592-020-0782-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/12/2020] [Indexed: 12/17/2022]
Abstract
Photobleaching limits extended imaging of fluorescent biological samples. Here, we developed DNA based “FluoroCubes” that are similar in size to the green fluorescent protein (GFP), have single-point attachment to proteins, have a ~54-fold higher photobleaching lifetime and emit ~43-fold more photons than single organic dyes. We demonstrate that DNA FluoroCubes provide outstanding tools for single-molecule imaging, allowing the tracking of single motor proteins for >800 steps with nanometer precision.
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15
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Niekamp S, Coudray N, Zhang N, Vale RD, Bhabha G. Coupling of ATPase activity, microtubule binding, and mechanics in the dynein motor domain. EMBO J 2019; 38:e101414. [PMID: 31268607 PMCID: PMC6600642 DOI: 10.15252/embj.2018101414] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
The movement of a molecular motor protein along a cytoskeletal track requires communication between enzymatic, polymer-binding, and mechanical elements. Such communication is particularly complex and not well understood in the dynein motor, an ATPase that is comprised of a ring of six AAA domains, a large mechanical element (linker) spanning over the ring, and a microtubule-binding domain (MTBD) that is separated from the AAA ring by a ~ 135 Å coiled-coil stalk. We identified mutations in the stalk that disrupt directional motion, have microtubule-independent hyperactive ATPase activity, and nucleotide-independent low affinity for microtubules. Cryo-electron microscopy structures of a mutant that uncouples ATPase activity from directional movement reveal that nucleotide-dependent conformational changes occur normally in one-half of the AAA ring, but are disrupted in the other half. The large-scale linker conformational change observed in the wild-type protein is also inhibited, revealing that this conformational change is not required for ATP hydrolysis. These results demonstrate an essential role of the stalk in regulating motor activity and coupling conformational changes across the two halves of the AAA ring.
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Affiliation(s)
- Stefan Niekamp
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Nicolas Coudray
- Department of Cell BiologySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
- Applied Bioinformatics LaboratoriesNew York University School of MedicineNew YorkNYUSA
| | - Nan Zhang
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Ronald D Vale
- Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California San FranciscoSan FranciscoCAUSA
| | - Gira Bhabha
- Department of Cell BiologySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
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Bridging the nanoscale measurement gap. Nat Methods 2019; 16:284. [DOI: 10.1038/s41592-019-0378-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Nanometer-accuracy distance measurements between fluorophores at the single-molecule level. Proc Natl Acad Sci U S A 2019; 116:4275-4284. [PMID: 30770448 PMCID: PMC6410877 DOI: 10.1073/pnas.1815826116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Measurements of macromolecular shapes provide insight into the mechanism of molecular machines. Distance measurements at the scale of biological macromolecules are often pursued by single-molecule fluorescence techniques. However, while single-molecule Förster resonance energy transfer can estimate distances of less than 8 nm, distances on the scale of 8 to 25 nm are difficult to determine. Here, we report two-color fluorescent distance measurement techniques capable of determining distances with ∼1-nm accuracy over a wide range of length scales. These methods can be implemented in high throughput on commonly available microscopes. As an example of their utility, we used our methods to uncover an unexpected conformational change in the antiparallel coiled-coil stalk of the dynein motor domain in different nucleotide states. Light microscopy is a powerful tool for probing the conformations of molecular machines at the single-molecule level. Single-molecule Förster resonance energy transfer can measure intramolecular distance changes of single molecules in the range of 2 to 8 nm. However, current superresolution measurements become error-prone below 25 nm. Thus, new single-molecule methods are needed for measuring distances in the 8- to 25-nm range. Here, we describe methods that utilize information about localization and imaging errors to measure distances between two different color fluorophores with ∼1-nm accuracy at distances >2 nm. These techniques can be implemented in high throughput using a standard total internal reflection fluorescence microscope and open-source software. We applied our two-color localization method to uncover an unexpected ∼4-nm nucleotide-dependent conformational change in the coiled-coil “stalk” of the motor protein dynein. We anticipate that these methods will be useful for high-accuracy distance measurements of single molecules over a wide range of length scales.
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