1
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Kusumi A, Tsunoyama TA, Suzuki KGN, Fujiwara TK, Aladag A. Transient, nano-scale, liquid-like molecular assemblies coming of age. Curr Opin Cell Biol 2024; 89:102394. [PMID: 38963953 DOI: 10.1016/j.ceb.2024.102394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 07/06/2024]
Abstract
This review examines the dynamic mechanisms underlying cellular signaling, communication, and adhesion via transient, nano-scale, liquid-like molecular assemblies on the plasma membrane (PM). Traditional views posit that stable, solid-like molecular complexes perform these functions. However, advanced imaging reveals that many signaling and scaffolding proteins only briefly reside in these molecular complexes and that micron-scale protein assemblies on the PM, including cell adhesion structures and synapses, are likely made of archipelagoes of nanoliquid protein islands. Borrowing the concept of liquid-liquid phase separation to form micron-scale biocondensates, we propose that these nano-scale oligomers and assemblies are enabled by multiple weak but specific molecular interactions often involving intrinsically disordered regions. The signals from individual nanoliquid signaling complexes would occur as pulses. Single-molecule imaging emerges as a crucial technique for characterizing these transient nanoliquid assemblies on the PM, suggesting a shift toward a model where the fluidity of interactions underpins signal regulation and integration.
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Affiliation(s)
- Akihiro Kusumi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.
| | - Taka A Tsunoyama
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Kenichi G N Suzuki
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan; Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1193, Japan; National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takahiro K Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Amine Aladag
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
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2
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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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3
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Schirripa Spagnolo C, Luin S. Impact of temporal resolution in single particle tracking analysis. DISCOVER NANO 2024; 19:87. [PMID: 38724858 PMCID: PMC11082114 DOI: 10.1186/s11671-024-04029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Temporal resolution is a key parameter in the observation of dynamic processes, as in the case of single molecules motions visualized in real time in two-dimensions by wide field (fluorescence) microscopy, but a systematic investigation of its effects in all the single particle tracking analysis steps is still lacking. Here we present tools to quantify its impact on the estimation of diffusivity and of its distribution using one of the most popular tracking software for biological applications on simulated data and movies. We found important shifts and different widths for diffusivity distributions, depending on the interplay of temporal sampling conditions with various parameters, such as simulated diffusivity, density of spots, signal-to-noise ratio, lengths of trajectories, and kind of boundaries in the simulation. We examined conditions starting from the ones of experiments on the fluorescently labelled receptor p75NTR, a relatively fast-diffusing membrane receptor (diffusivity around 0.5-1 µm2/s), visualized by TIRF microscopy on the basal membrane of living cells. From the analysis of the simulations, we identified the best conditions in cases similar to these ones; considering also the experiments, we could confirm a range of values of temporal resolution suitable for obtaining reliable diffusivity results. The procedure we present can be exploited in different single particle/molecule tracking applications to find an optimal temporal resolution.
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Affiliation(s)
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127, Pisa, Italy.
- NEST Laboratory, Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127, Pisa, Italy.
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4
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Dukhno O, Ghosh S, Greiner V, Bou S, Godet J, Muhr V, Buchner M, Hirsch T, Mély Y, Przybilla F. Targeted Single Particle Tracking with Upconverting Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2024; 16:11217-11227. [PMID: 38386424 DOI: 10.1021/acsami.3c17116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Single particle tracking (SPT) is a powerful technique for real-time microscopic visualization of the movement of individual biomolecules within or on the surface of living cells. However, SPT often suffers from the suboptimal performance of the photon-emitting labels used to tag the biomolecules of interest. For example, fluorescent dyes have poor photostability, while quantum dots suffer from blinking that hampers track acquisition and interpretation. Upconverting nanoparticles (UCNPs) have recently emerged as a promising anti-Stokes luminescent label for SPT. In this work, we demonstrated targeted SPT using UCNPs. For this, we synthesized 30 nm diameter doped UCNPs and coated them with amphiphilic polymers decorated with polyethylene glycol chains to make them water-dispersible and minimize their nonspecific interactions with cells. Coated UCNPs highly homogeneous in brightness (as confirmed by a single particle investigation) were functionalized by immunoglobulin E (IgE) using a biotin-streptavidin strategy. Using these IgE-UCNP SPT labels, we tracked high-affinity IgE receptors (FcεRI) on the membrane of living RBL-2H3 mast cells at 37 °C in the presence and absence of antigen and obtained good agreement with the literature. Moreover, we used the FcεRI-IgE receptor-antibody system to directly compare the performance of UCNP-based SPT labels to organic dyes (AlexaFluor647) and quantum dots (QD655). Due to their photostability as well as their backgroundless and continuous luminescence, SPT trajectories obtained with UCNP labels are no longer limited by the photophysics of the label but only by the dynamics of the system and, in particular, the movement of the label out of the field of view and/or focal plane.
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Affiliation(s)
- Oleksii Dukhno
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Srijayee Ghosh
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Vanille Greiner
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Sophie Bou
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Julien Godet
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
- IMAGeS team at ICube, UMR 7357, CNRS, Université de Strasbourg, Strasbourg 67000, France
| | - Verena Muhr
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Markus Buchner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Thomas Hirsch
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
| | - Yves Mély
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
| | - Frédéric Przybilla
- Laboratory of Biomaging and Pathologies, UMR 7021 CNRS, University of Strasbourg, Strasbourg 67000, France
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5
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Yanagawa M, Shimobayashi SF. Multi-dimensional condensation of intracellular biomolecules. J Biochem 2024; 175:179-186. [PMID: 37993409 DOI: 10.1093/jb/mvad095] [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] [Received: 09/12/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023] Open
Abstract
Liquid-liquid phase separation has been recognized as universal mechanisms in living cells for the formation of RNA-protein condensates and ordered lipid domains. These biomolecular condensates or domains nucleate, diffuse and interact with each other across physical dimensions to perform their biological functions. Here we summarize key features of biophysical principles underlying the multi-dimensional condensation of RNA-protein condensates and ordered lipid domains, which are related to nuclear transcription, and signaling on cell membranes. Uncovering physicochemical factors that govern the spatiotemporal coupling of those condensates presents a new avenue in their functions and associated human diseases.
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Affiliation(s)
- Masataka Yanagawa
- Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shunsuke F Shimobayashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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6
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Zhang Q, Chai W, Pan X, Gai H. Amplification-Free Digital Immunoassay down to the Attomolar Level by Synergistic Sedimentation of Brownian Motion Suppression and Dehydration Transfer. Anal Chem 2024. [PMID: 38329294 DOI: 10.1021/acs.analchem.3c05066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Amplification-free digital immunoassays (DIAs) typically utilize optical nanoparticles to enhance single immunocomplex molecule detection. The efficiency and uniformity of transferring the nanoparticles from a bulk solution to a solid surface determine the limit of detection (LOD) and the accuracy of DIAs. Previous methods suffer from issues like low efficiency, nonuniform distribution, and particle aggregation. Here, we present a novel technique named synergistic sedimentation of Brownian motion suppression and dehydration transfer (SynSed) for nanoparticles using water-soluble polymers. The efficiency of transferring quantum dots (QDs) was increased from 10.7 to 91.4%, and the variation in QD distribution was restricted to 8.8%. By incorporating SynSed into DIAs, we achieved a remarkable reduction in the LOD (down to 3.9 aM) for carcinoembryonic antigen and expanded the dynamic range to cover 3 orders of magnitude in concentration, ranging from 0.01 to 10 fM. DIAs enhanced with SynSed possess ultrahigh sensitivity, advanced accuracy, and specificity, offering a great premise in early disease diagnostics, risk stratification, and treatment response monitoring.
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Affiliation(s)
- Qingquan Zhang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Wenwen Chai
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Xiaoyan Pan
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Hongwei Gai
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
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7
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Kæstel-Hansen J, Hatzakis NS. Everything, everywhere, almost at once. eLife 2024; 13:e95362. [PMID: 38285015 PMCID: PMC10824506 DOI: 10.7554/elife.95362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024] Open
Abstract
A new platform that can follow the movement of individual proteins inside millions of cells in a single day will help contribute to existing knowledge of cell biology and identify new therapeutics.
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Affiliation(s)
- Jacob Kæstel-Hansen
- Department of Chemistry, Novo Nordisk Foundation Center for Optimized Oligo Escape and Control of Disease, University of CopenhagenCopenhagenDenmark
| | - Nikos S Hatzakis
- Department of Chemistry, Novo Nordisk Foundation Center for Optimized Oligo Escape and Control of Disease, University of CopenhagenCopenhagenDenmark
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8
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Gormal RS, Martinez-Marmol R, Brooks AJ, Meunier FA. Location, location, location: Protein kinase nanoclustering for optimised signalling output. eLife 2024; 13:e93902. [PMID: 38206309 PMCID: PMC10783869 DOI: 10.7554/elife.93902] [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] [Received: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Protein kinases (PKs) are proteins at the core of cellular signalling and are thereby responsible for most cellular physiological processes and their regulations. As for all intracellular proteins, PKs are subjected to Brownian thermal energy that tends to homogenise their distribution throughout the volume of the cell. To access their substrates and perform their critical functions, PK localisation is therefore tightly regulated in space and time, relying upon a range of clustering mechanisms. These include post-translational modifications, protein-protein and protein-lipid interactions, as well as liquid-liquid phase separation, allowing spatial restriction and ultimately regulating access to their substrates. In this review, we will focus on key mechanisms mediating PK nanoclustering in physiological and pathophysiological processes. We propose that PK nanoclusters act as a cellular quantal unit of signalling output capable of integration and regulation in space and time. We will specifically outline the various super-resolution microscopy approaches currently used to elucidate the composition and mechanisms driving PK nanoscale clustering and explore the pathological consequences of altered kinase clustering in the context of neurodegenerative disorders, inflammation, and cancer.
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Affiliation(s)
- Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Ramon Martinez-Marmol
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Andrew J Brooks
- Frazer Institute, The University of QueenslandWoolloongabbaAustralia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
- School of Biomedical Sciences, The University of QueenslandSt LuciaAustralia
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9
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Walker G, Brown C, Ge X, Kumar S, Muzumdar MD, Gupta K, Bhattacharyya M. Oligomeric organization of membrane proteins from native membranes at nanoscale spatial and single-molecule resolution. NATURE NANOTECHNOLOGY 2024; 19:85-94. [PMID: 38012273 PMCID: PMC10981947 DOI: 10.1038/s41565-023-01547-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
The oligomeric organization of membrane proteins in native cell membranes is a critical regulator of their function. High-resolution quantitative measurements of oligomeric assemblies and how they change under different conditions are indispensable to understanding membrane protein biology. We report Native-nanoBleach, a total internal reflection fluorescence microscopy-based single-molecule photobleaching step analysis technique to determine the oligomeric distribution of membrane proteins directly from native membranes at an effective spatial resolution of ~10 nm. We achieved this by capturing target membrane proteins in native nanodiscs with their proximal native membrane environment using amphipathic copolymers. We applied Native-nanoBleach to quantify the oligomerization status of structurally and functionally diverse membrane proteins, including a receptor tyrosine kinase (TrkA) and a small GTPase (KRas) under growth-factor binding and oncogenic mutations, respectively. Our data suggest that Native-nanoBleach provides a sensitive, single-molecule platform to quantify membrane protein oligomeric distributions in native membranes under physiologically and clinically relevant conditions.
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Affiliation(s)
- Gerard Walker
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Caroline Brown
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Xiangyu Ge
- Department of Pathology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Shailesh Kumar
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Mandar D Muzumdar
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
- Department of Genetics, Yale University, New Haven, CT, USA
- Department of Internal Medicine, Yale University, New Haven, CT, USA
- Yale Cancer Center, New Haven, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
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10
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Waigh TA, Korabel N. Heterogeneous anomalous transport in cellular and molecular biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023; 86:126601. [PMID: 37863075 DOI: 10.1088/1361-6633/ad058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 10/20/2023] [Indexed: 10/22/2023]
Abstract
It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballistic transport. Recent research demonstrates that anomalous transport is in many cases heterogeneous in both time and space. Thus single anomalous exponents and single generalised diffusion coefficients are unable to satisfactorily describe many crucial phenomena in cellular and molecular biology. We consider advances in the field ofheterogeneous anomalous transport(HAT) highlighting: experimental techniques (single molecule methods, microscopy, image analysis, fluorescence correlation spectroscopy, inelastic neutron scattering, and nuclear magnetic resonance), theoretical tools for data analysis (robust statistical methods such as first passage probabilities, survival analysis, different varieties of mean square displacements, etc), analytic theory and generative theoretical models based on simulations. Special emphasis is made on high throughput analysis techniques based on machine learning and neural networks. Furthermore, we consider anomalous transport in the context of microrheology and the heterogeneous viscoelasticity of complex fluids. HAT in the wavefronts of reaction-diffusion systems is also considered since it plays an important role in morphogenesis and signalling. In addition, we present specific examples from cellular biology including embryonic cells, leucocytes, cancer cells, bacterial cells, bacterial biofilms, and eukaryotic microorganisms. Case studies from molecular biology include DNA, membranes, endosomal transport, endoplasmic reticula, mucins, globular proteins, and amyloids.
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Affiliation(s)
- Thomas Andrew Waigh
- Biological Physics, School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, United Kingdom
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11
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Chen Z, Seman M, Farhat A, Fyodorova Y, Biswas S, Levashkevich A, Freddolino PL, Biteen JS, Ragunathan K. Tracking live-cell single-molecule dynamics enables measurements of heterochromatinassociated protein-protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531771. [PMID: 36945633 PMCID: PMC10028927 DOI: 10.1101/2023.03.08.531771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy enables high-resolution and sensitive imaging of the positions and movement of molecules in living cells. HP1 proteins are important regulators of gene expression because they selectively bind and recognize H3K9 methylated (H3K9me) histones to form heterochromatin-associated protein complexes that silence gene expression. Here, we extended live-cell single-molecule tracking studies in fission yeast to determine how HP1 proteins interact with their binding partners in the nucleus. We measured how genetic perturbations that affect H3K9me alter the diffusive properties of HP1 proteins and each of their binding partners based on which we inferred their most likely interaction sites. Our results indicate that H3K9me promotes specific complex formation between HP1 proteins and their interactors in a spatially restricted manner, while attenuating their ability to form off-chromatin complexes. As opposed to being an inert platform or scaffold to direct HP1 binding, our studies propose a novel function for H3K9me as an active participant in enhancing HP1-associated complex formation in living cells.
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Affiliation(s)
- Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
| | - Melissa Seman
- Department of Biology, Brandeis University, Waltham, MA 02451 USA
| | - Ali Farhat
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Saikat Biswas
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48104 USA
- Current address: Pacific Biosciences, Menlo Park, CA 94025, USA
| | | | - P. Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48104 USA
| | - Julie S. Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48104 USA
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12
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Mayor S, Bhat A, Kusumi A. A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization. Cold Spring Harb Perspect Biol 2023; 15:a041394. [PMID: 37643877 PMCID: PMC10547391 DOI: 10.1101/cshperspect.a041394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.
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Affiliation(s)
- Satyajit Mayor
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Abrar Bhat
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Akihiro Kusumi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
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13
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Karam J, Singer BJ, Miwa H, Chen LH, Maran K, Hasani M, Garza S, Onyekwere B, Yeh HC, Li S, Carlo DD, Seidlits SK. Molecular weight of hyaluronic acid crosslinked into biomaterial scaffolds affects angiogenic potential. Acta Biomater 2023; 169:228-242. [PMID: 37572983 DOI: 10.1016/j.actbio.2023.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
While hyaluronic acid (HA)-based hydrogels have been used clinically for decades, the mechanisms by which HA exerts molecular weight-dependent bioactivity and how chemical modification and crosslinking may affect molecular weight-dependent bioactivity remain poorly understood. This knowledge gap presents a significant barrier to designing HA hydrogels with predictable bioactivities. As HA has been widely reported to have molecular weight-dependent effects on endothelial cells (ECs), we investigated how the molecular weight of HA in either soluble or crosslinked forms affects angiogenesis and interrogated CD44 clustering on the surface of endothelial cells as a candidate mechanism for these affects. Using soluble HA, our results show high molecular weight (HMW) HA, but not low molecular weight (LMW) HA, increased viability and tube formation in cultured human cerebral microvascular ECs (HCMVECs). No size of HA affected proliferation. When HCMVECs were cultured with crosslinked HA of varying molecular weights in the form of HA-based microporous annealed particle scaffold (HMAPS), the cell response was comparable to when cultured with soluble HA. Similarly, when implanted subcutaneously, HMAPS with HMW HA were more vascularized than those with LMW HA. We also show that antibody-mediated CD44 clustering resulted in HCMVECs with increased viability and tube-like structure formation in a manner comparable to exposure to HMW HA, suggesting that HMW acts through CD44 clustering. STATEMENT OF SIGNIFICANCE: Biomaterials based on hyaluronic acid (HA), a bioactive extracellular matrix polysaccharide, have been used in clinical products for several years. Despite the knowledge that HA molecular weight heavily influences its bioactivity, molecular weight has been largely ignored in the development of HA-based biomaterials. Given the high viscosity of high molecular weight HA typically found in native tissues, lower molecular weight polysaccharides have been used most commonly for biomaterial fabrication. By comparing the ability of injectable, microporous annealed particle scaffolds (MAPS) fabricated from variably sized HA to promote angiogenesis, this study demonstrates that MAPS with high molecular weight HA better support vascularization, likely through an unique ability to induce clustering of CD44 receptors on endothelial cells.
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Affiliation(s)
- Josh Karam
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Breahna J Singer
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hiromi Miwa
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Limin H Chen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kajal Maran
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Mahdi Hasani
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Sarahi Garza
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Bianca Onyekwere
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA; Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Stephanie K Seidlits
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
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14
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Farinha JPS. Bright and Stable Nanomaterials for Imaging and Sensing. Polymers (Basel) 2023; 15:3935. [PMID: 37835984 PMCID: PMC10575272 DOI: 10.3390/polym15193935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
This review covers strategies to prepare high-performance emissive polymer nanomaterials, combining very high brightness and photostability, to respond to the drive for better imaging quality and lower detection limits in fluorescence imaging and sensing applications. The more common approaches to obtaining high-brightness nanomaterials consist of designing polymer nanomaterials carrying a large number of fluorescent dyes, either by attaching the dyes to individual polymer chains or by encapsulating the dyes in nanoparticles. In both cases, the dyes can be covalently linked to the polymer during polymerization (by using monomers functionalized with fluorescent groups), or they can be incorporated post-synthesis, using polymers with reactive groups, or encapsulating the unmodified dyes. Silica nanoparticles in particular, obtained by the condensation polymerization of silicon alcoxides, provide highly crosslinked environments that protect the dyes from photodegradation and offer excellent chemical modification flexibility. An alternative and less explored strategy is to increase the brightness of each individual dye. This can be achieved by using nanostructures that couple dyes to plasmonic nanoparticles so that the plasmon resonance can act as an electromagnetic field concentrator to increase the dye excitation efficiency and/or interact with the dye to increase its emission quantum yield.
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Affiliation(s)
- José Paulo Sequeira Farinha
- Centro de Química Estrutural, Institute of Molecular Sciences and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
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15
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Zalejski J, Sun J, Sharma A. Unravelling the Mystery inside Cells by Using Single-Molecule Fluorescence Imaging. J Imaging 2023; 9:192. [PMID: 37754956 PMCID: PMC10532472 DOI: 10.3390/jimaging9090192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Live-cell imaging is a powerful technique to study the dynamics and mechanics of various biological molecules like proteins, organelles, DNA, and RNA. With the rapid evolution of optical microscopy, our understanding of how these molecules are implicated in the cells' most critical physiological roles deepens. In this review, we focus on how spatiotemporal nanoscale live-cell imaging at the single molecule level allows for profound contributions towards new discoveries in life science. This review will start by summarizing how single-molecule tracking has been used to analyze membrane dynamics, receptor-ligand interactions, protein-protein interactions, inner- and extra-cellular transport, gene expression/transcription, and whole organelle tracking. We then move on to how current authors are trying to improve single-molecule tracking and overcome current limitations by offering new ways of labeling proteins of interest, multi-channel/color detection, improvements in time-lapse imaging, and new methods and programs to analyze the colocalization and movement of targets. We later discuss how single-molecule tracking can be a beneficial tool used for medical diagnosis. Finally, we wrap up with the limitations and future perspectives of single-molecule tracking and total internal reflection microscopy.
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Affiliation(s)
| | | | - Ashutosh Sharma
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA; (J.Z.); (J.S.)
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16
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Huang Z, Kanchanawong P. Ultra high-speed single-molecule fluorescence imaging. J Cell Biol 2023; 222:e202306136. [PMID: 37458726 PMCID: PMC10351246 DOI: 10.1083/jcb.202306136] [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] [Indexed: 07/20/2023] Open
Abstract
In two articles in this issue, Fujiwara et al. developed an ultrasensitive high-speed camera capable of single-molecule fluorescence imaging at a microsecond timescale (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202110160). This major leap in detection speed enables the organization of plasma membrane and integrin-based adhesions to be probed in unprecedented detail (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202110162).
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Affiliation(s)
- Zengxin Huang
- Mechanobiology Institute, National University of Singapore, Singapore, Republic of Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Republic of Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore, Republic of Singapore
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17
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Niederauer C, Nguyen C, Wang-Henderson M, Stein J, Strauss S, Cumberworth A, Stehr F, Jungmann R, Schwille P, Ganzinger KA. Dual-color DNA-PAINT single-particle tracking enables extended studies of membrane protein interactions. Nat Commun 2023; 14:4345. [PMID: 37468504 DOI: 10.1038/s41467-023-40065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
DNA-PAINT based single-particle tracking (DNA-PAINT-SPT) has recently significantly enhanced observation times in in vitro SPT experiments by overcoming the constraints of fluorophore photobleaching. However, with the reported implementation, only a single target can be imaged and the technique cannot be applied straight to live cell imaging. Here we report on leveraging this technique from a proof-of-principle implementation to a useful tool for the SPT community by introducing simultaneous live cell dual-color DNA-PAINT-SPT for quantifying protein dimerization and tracking proteins in living cell membranes, demonstrating its improved performance over single-dye SPT.
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Affiliation(s)
| | - Chikim Nguyen
- Autonomous Matter Department, AMOLF, Amsterdam, The Netherlands
| | | | - Johannes Stein
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | - Florian Stehr
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics, Ludwig Maximilian University, Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried, Germany
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18
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Nguyen TD, Chen YI, Chen LH, Yeh HC. Recent Advances in Single-Molecule Tracking and Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:253-284. [PMID: 37314878 DOI: 10.1146/annurev-anchem-091922-073057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.
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Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Limin H Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Texas Materials Institute, University of Texas at Austin, Austin, Texas, USA
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19
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Wallis TP, Jiang A, Young K, Hou H, Kudo K, McCann AJ, Durisic N, Joensuu M, Oelz D, Nguyen H, Gormal RS, Meunier FA. Super-resolved trajectory-derived nanoclustering analysis using spatiotemporal indexing. Nat Commun 2023; 14:3353. [PMID: 37291117 PMCID: PMC10250379 DOI: 10.1038/s41467-023-38866-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/11/2023] [Indexed: 06/10/2023] Open
Abstract
Single-molecule localization microscopy techniques are emerging as vital tools to unravel the nanoscale world of living cells by understanding the spatiotemporal organization of protein clusters at the nanometer scale. Current analyses define spatial nanoclusters based on detections but neglect important temporal information such as cluster lifetime and recurrence in "hotspots" on the plasma membrane. Spatial indexing is widely used in video games to detect interactions between moving geometric objects. Here, we use the R-tree spatial indexing algorithm to determine the overlap of the bounding boxes of individual molecular trajectories to establish membership in nanoclusters. Extending the spatial indexing into the time dimension allows the resolution of spatial nanoclusters into multiple spatiotemporal clusters. Using spatiotemporal indexing, we found that syntaxin1a and Munc18-1 molecules transiently cluster in hotspots, offering insights into the dynamics of neuroexocytosis. Nanoscale spatiotemporal indexing clustering (NASTIC) has been implemented as a free and open-source Python graphic user interface.
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Affiliation(s)
- Tristan P Wallis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Anmin Jiang
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kyle Young
- School of Mathematics and Physics, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Huiyi Hou
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kye Kudo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Alex J McCann
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dietmar Oelz
- School of Mathematics and Physics, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Hien Nguyen
- School of Mathematics and Physics, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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20
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Chhabra Y, Seiffert P, Gormal RS, Vullings M, Lee CMM, Wallis TP, Dehkhoda F, Indrakumar S, Jacobsen NL, Lindorff-Larsen K, Durisic N, Waters MJ, Meunier FA, Kragelund BB, Brooks AJ. Tyrosine kinases compete for growth hormone receptor binding and regulate receptor mobility and degradation. Cell Rep 2023; 42:112490. [PMID: 37163374 DOI: 10.1016/j.celrep.2023.112490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/07/2023] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
Growth hormone (GH) acts via JAK2 and LYN to regulate growth, metabolism, and neural function. However, the relationship between these tyrosine kinases remains enigmatic. Through an interdisciplinary approach combining cell biology, structural biology, computation, and single-particle tracking on live cells, we find overlapping LYN and JAK2 Box1-Box2-binding regions in GH receptor (GHR). Our data implicate direct competition between JAK2 and LYN for GHR binding and imply divergent signaling profiles. We show that GHR exhibits distinct mobility states within the cell membrane and that activation of LYN by GH mediates GHR immobilization, thereby initiating its nanoclustering in the membrane. Importantly, we observe that LYN mediates cytokine receptor degradation, thereby controlling receptor turnover and activity, and this applies to related cytokine receptors. Our study offers insight into the molecular interactions of LYN with GHR and highlights important functions for LYN in regulating GHR nanoclustering, signaling, and degradation, traits broadly relevant to many cytokine receptors.
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Affiliation(s)
- Yash Chhabra
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia; The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21204, USA.
| | - Pernille Seiffert
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rachel S Gormal
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Manon Vullings
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia
| | | | - Tristan P Wallis
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Farhad Dehkhoda
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Sowmya Indrakumar
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nina L Jacobsen
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nela Durisic
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J Waters
- The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia
| | - Frédéric A Meunier
- The Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNLab) and REPIN, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Andrew J Brooks
- Frazer Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia; The University of Queensland, Institute for Molecular Bioscience, St. Lucia, QLD 4072, Australia.
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21
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Simon F, Tinevez JY, van Teeffelen S. ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks. J Cell Biol 2023; 222:e202208059. [PMID: 36880553 PMCID: PMC9997658 DOI: 10.1083/jcb.202208059] [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: 08/14/2022] [Revised: 12/01/2022] [Accepted: 01/27/2023] [Indexed: 03/08/2023] Open
Abstract
Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.
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Affiliation(s)
- François Simon
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Sven van Teeffelen
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
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22
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Simon F, Tinevez JY, van Teeffelen S. ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks. J Cell Biol 2023; 222:e202208059. [PMID: 36880553 PMCID: PMC9997658 DOI: 10.1083/jcb.202208059 10.1101/2022.07.13.499913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/01/2022] [Accepted: 01/27/2023] [Indexed: 03/23/2024] Open
Abstract
Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.
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Affiliation(s)
- François Simon
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Sven van Teeffelen
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
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23
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Kim J, Lee S, Lee YK, Seong B, Kim HM, Kyeong S, Kim W, Ham K, Pham XH, Hahm E, Mun JY, Safaa MA, Lee YS, Jun BH, Park HS. In Vitro Tracking of Human Umbilical Vein Endothelial Cells Using Ultra-Sensitive Quantum Dot-Embedded Silica Nanoparticles. Int J Mol Sci 2023; 24:ijms24065794. [PMID: 36982869 PMCID: PMC10052325 DOI: 10.3390/ijms24065794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The nanoscale spatiotemporal resolution of single-particle tracking (SPT) renders it a powerful method for exploring single-molecule dynamics in living cells or tissues, despite the disadvantages of using traditional organic fluorescence probes, such as the weak fluorescent signal against the strong cellular autofluorescence background coupled with a fast-photobleaching rate. Quantum dots (QDs), which enable tracking targets in multiple colors, have been proposed as an alternative to traditional organic fluorescence dyes; however, they are not ideally suitable for applying SPT due to their hydrophobicity, cytotoxicity, and blinking problems. This study reports an improved SPT method using silica-coated QD-embedded silica nanoparticles (QD2), which represent brighter fluorescence and are less toxic than single QDs. After treatment of QD2 in 10 μg/mL, the label was retained for 96 h with 83.76% of labeling efficiency, without impaired cell function such as angiogenesis. The improved stability of QD2 facilitates the visualization of in situ endothelial vessel formation without real-time staining. Cells retain QD2 fluorescence signal for 15 days at 4 °C without significant photobleaching, indicating that QD2 has overcome the limitations of SPT enabling long-term intracellular tracking. These results proved that QD2 could be used for SPT as a substitute for traditional organic fluorophores or single quantum dots, with its photostability, biocompatibility, and superior brightness.
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Affiliation(s)
- Jaehi Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Sunray Lee
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | - Yeon Kyung Lee
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | - Bomi Seong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyung-Mo Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - San Kyeong
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Wooyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Kyeongmin Ham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Xuan-Hung Pham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Eunil Hahm
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Ji Yeon Mun
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | | | - Yoon-Sik Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyun-Sook Park
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
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24
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Makkai G, Abraham IM, Barabas K, Godo S, Ernszt D, Kovacs T, Kovacs G, Szocs S, Janosi TZ. Maximum likelihood-based estimation of diffusion coefficient is quick and reliable method for analyzing estradiol actions on surface receptor movements. Front Neuroinform 2023; 17:1005936. [PMID: 36970656 PMCID: PMC10031098 DOI: 10.3389/fninf.2023.1005936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
The rapid effects of estradiol on membrane receptors are in the focus of the estradiol research field, however, the molecular mechanisms of these non-classical estradiol actions are poorly understood. Since the lateral diffusion of membrane receptors is an important indicator of their function, a deeper understanding of the underlying mechanisms of non-classical estradiol actions can be achieved by investigating receptor dynamics. Diffusion coefficient is a crucial and widely used parameter to characterize the movement of receptors in the cell membrane. The aim of this study was to investigate the differences between maximum likelihood-based estimation (MLE) and mean square displacement (MSD) based calculation of diffusion coefficients. In this work we applied both MSD and MLE to calculate diffusion coefficients. Single particle trajectories were extracted from simulation as well as from α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor tracking in live estradiol-treated differentiated PC12 (dPC12) cells. The comparison of the obtained diffusion coefficients revealed the superiority of MLE over the generally used MSD analysis. Our results suggest the use of the MLE of diffusion coefficients because as it has a better performance, especially for large localization errors or slow receptor movements.
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Affiliation(s)
- Geza Makkai
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Nano-Bio-Imaging Core Facility at the Szentágothai Research Centre of the University of Pécs, Pécs, Hungary
| | - Istvan M. Abraham
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Klaudia Barabas
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Soma Godo
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - David Ernszt
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Tamas Kovacs
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gergely Kovacs
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Szilard Szocs
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
| | - Tibor Z. Janosi
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Nano-Bio-Imaging Core Facility at the Szentágothai Research Centre of the University of Pécs, Pécs, Hungary
- *Correspondence: Tibor Z. Janosi,
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25
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Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023; 51:557-569. [PMID: 36876879 DOI: 10.1042/bst20221242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we describe how SMT works, what it can tell us about molecular biology, and how it has changed our perspective on the inner workings of the nucleus. We also describe what SMT cannot yet tell us and how new technical advances seek to overcome its limitations. This ongoing progress will be imperative to address outstanding questions about how dynamic molecular machines function in live cells.
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26
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Du Y, Lyu Y, Li S, Ding D, Chen J, Yang C, Sun Y, Qu F, Xiao Z, Jiang J, Tan W. Ligand Dilution Analysis Facilitates Aptamer Binding Characterization at the Single-Molecule Level. Angew Chem Int Ed Engl 2023; 62:e202215387. [PMID: 36479802 DOI: 10.1002/anie.202215387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
Cell-specific aptamers offer a powerful tool to study membrane receptors at the single-molecule level. Most target receptors of aptamers are highly expressed on the cell surface, but difficult to analyze in situ because of dense distribution and fast velocity. Therefore, we herein propose a random sampling-based analysis strategy termed ligand dilution analysis (LDA) for easily implemented aptamer-based receptor study. Receptor density on the cell surface can be calculated based on a regression model. By using a synergistic ligand dilution design, colocalization and differentiation of aptamer and monoclonal antibody (mAb) binding on a single receptor can be realized. Once this is accomplished, precise binding site and detailed aptamer-receptor binding mode can be further determined using molecular docking and molecular dynamics simulation. The ligand dilution strategy also sets the stage for an aptamer-based dynamics analysis of two- and three-dimensional motion and fluctuation of highly expressed receptors on the live cell membrane.
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Affiliation(s)
- Yulin Du
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Shenzhen Research Institute, Hunan University, Shenzhen, Guangdong 518000, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ding Ding
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianghuai Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cai Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fengli Qu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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27
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Walker G, Brown C, Ge X, Kumar S, Muzumdar MD, Gupta K, Bhattacharyya M. Determination of oligomeric organization of membrane proteins from native membranes at nanoscale-spatial and single-molecule resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.529138. [PMID: 36865290 PMCID: PMC9980011 DOI: 10.1101/2023.02.19.529138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The oligomeric organization of membrane proteins in native cell membranes is a critical regulator of their function. High-resolution quantitative measurements of oligomeric assemblies and how they change under different conditions are indispensable to the understanding of membrane protein biology. We report a single-molecule imaging technique (Native-nanoBleach) to determine the oligomeric distribution of membrane proteins directly from native membranes at an effective spatial resolution of ∼10 nm. We achieved this by capturing target membrane proteins in "native nanodiscs" with their proximal native membrane environment using amphipathic copolymers. We established this method using structurally and functionally diverse membrane proteins with well-established stoichiometries. We then applied Native-nanoBleach to quantify the oligomerization status of a receptor tyrosine kinase (TrkA) and a small GTPase (KRas) under conditions of growth-factor binding or oncogenic mutations, respectively. Native-nanoBleach provides a sensitive, single-molecule platform to quantify membrane protein oligomeric distributions in native membranes at an unprecedented spatial resolution.
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28
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Teng M, Li Z, Zhou Y, Zhang Z, Miao L, Bai X, Li Y, Wang S. Real-Time Monitoring of CAR-T Cell Efficiency through a Biorthogonal Cycloaddition Labeling Strategy. Bioconjug Chem 2023; 34:443-452. [PMID: 36748916 DOI: 10.1021/acs.bioconjchem.3c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chimeric antigen receptors (CARs) recognizing tumor-associated antigens (TAAs) effectively target tumor cells without using the major histocompatibility complex (MHC). However, CARs have inaccurate dose determination in clinical practice, and the methods that can solve this problem often produce cytotoxic substances, such as green fluorescent protein (GFP) insertion. Therefore, in this study, we tried to anchor harmless fluorescent labels on CAR-T cell membranes using highly biologically compatible strain-promoted alkyne-azide cycloaddition (SPAAC) without any byproducts. Our conjugated fluorescent label was stable on the CAR-T cell surface for at least two weeks, with excellent light stability and metrology. Also, this method enabled the rapid quantification of the living CAR-T cells without affecting their activity. Thus, this method is a promising reliable strategy for accurately diagnosing and treating cancer.
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Affiliation(s)
- Muzhou Teng
- Key Laboratory of the Digestive System Tumors of Gansu Province, The Second Clinical Medical College of Lanzhou University, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Zhijia Li
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yali Zhou
- Key Laboratory of the Digestive System Tumors of Gansu Province, The Second Clinical Medical College of Lanzhou University, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Zhengchao Zhang
- Key Laboratory of the Digestive System Tumors of Gansu Province, The Second Clinical Medical College of Lanzhou University, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Lele Miao
- Key Laboratory of the Digestive System Tumors of Gansu Province, The Second Clinical Medical College of Lanzhou University, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Xiao Bai
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
| | - Yumin Li
- Key Laboratory of the Digestive System Tumors of Gansu Province, The Second Clinical Medical College of Lanzhou University, Lanzhou University Second Hospital, Lanzhou 730000, China
| | - Song Wang
- Key Laboratory of the Digestive System Tumors of Gansu Province, The Second Clinical Medical College of Lanzhou University, Lanzhou University Second Hospital, Lanzhou 730000, China
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29
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Takebayashi K, Kamimura Y, Ueda M. Field model for multistate lateral diffusion of various transmembrane proteins observed in living Dictyostelium cells. J Cell Sci 2023; 136:286715. [PMID: 36655427 PMCID: PMC10022678 DOI: 10.1242/jcs.260280] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
The lateral diffusion of transmembrane proteins on plasma membranes is a fundamental process for various cellular functions. Diffusion properties specific for individual protein species have been extensively studied, but the common features among protein species are poorly understood. Here, we systematically studied the lateral diffusion of various transmembrane proteins in the lower eukaryote Dictyostelium discoideum cells using a hidden Markov model for single-molecule trajectories obtained experimentally. As common features, all membrane proteins that had from one to ten transmembrane regions adopted three free diffusion states with similar diffusion coefficients regardless of their structural variability. All protein species reduced their mobility similarly upon the inhibition of microtubule or actin cytoskeleton dynamics, or myosin II. The relationship between protein size and the diffusion coefficient was consistent with the Saffman-Delbrück model, meaning that membrane viscosity is a major determinant of lateral diffusion, but protein size is not. These protein species-independent properties of multistate free diffusion were explained simply and quantitatively by free diffusion on the three membrane regions with different viscosities, which is in sharp contrast to the complex diffusion behavior of transmembrane proteins in higher eukaryotes.
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Affiliation(s)
- Kazutoshi Takebayashi
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.,Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Yoichiro Kamimura
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Masahiro Ueda
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.,Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
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30
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Xu C, Yang K, Yuan B. Non-Gaussian Diffusion of Individual Lipids Unveils the Unique Peptide-Membrane Interaction Dynamics. J Phys Chem Lett 2023; 14:854-862. [PMID: 36656807 DOI: 10.1021/acs.jpclett.2c03467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The dynamics of protein (or peptide)-membrane interactions plays a central role in cellular functions; however, the underlying mechanisms remain unclear. Herein, through analyzing the diffusion of individual lipids in a bilayer membrane during the membrane actions of typical peptides (e.g., pore-forming peptide melittin and cell-penetrating peptide TAT) at varying concentrations, the spatial heterogeneity as well as temporal dynamics of lipid motions were investigated which showed close correlation with the peptide action mechanism. Specifically, the spatial heterogeneity of lipid diffusion was characterized by the non-Gaussianity of lipid trajectories, which was further decomposed into two basic diffusion modes; moreover, the temporal evolution of the Gaussian fitting parameters provided quantitative information on the varying metastable interaction states between peptides and the membrane (e.g., peptide landing, membrane insertion, and equilibrium). Generally, this work gives an insight into the correlation between single-lipid diffusion and function-realization of membrane-active peptides.
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Affiliation(s)
- Cheng Xu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou215006, Jiangsu, China
- Songshan Lake Materials Laboratory, Dongguan523808, Guangdong, China
| | - Kai Yang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou215006, Jiangsu, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan523808, Guangdong, China
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31
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Kanchanawong P, Calderwood DA. Organization, dynamics and mechanoregulation of integrin-mediated cell-ECM adhesions. Nat Rev Mol Cell Biol 2023; 24:142-161. [PMID: 36168065 PMCID: PMC9892292 DOI: 10.1038/s41580-022-00531-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2022] [Indexed: 02/04/2023]
Abstract
The ability of animal cells to sense, adhere to and remodel their local extracellular matrix (ECM) is central to control of cell shape, mechanical responsiveness, motility and signalling, and hence to development, tissue formation, wound healing and the immune response. Cell-ECM interactions occur at various specialized, multi-protein adhesion complexes that serve to physically link the ECM to the cytoskeleton and the intracellular signalling apparatus. This occurs predominantly via clustered transmembrane receptors of the integrin family. Here we review how the interplay of mechanical forces, biochemical signalling and molecular self-organization determines the composition, organization, mechanosensitivity and dynamics of these adhesions. Progress in the identification of core multi-protein modules within the adhesions and characterization of rearrangements of their components in response to force, together with advanced imaging approaches, has improved understanding of adhesion maturation and turnover and the relationships between adhesion structures and functions. Perturbations of adhesion contribute to a broad range of diseases and to age-related dysfunction, thus an improved understanding of their molecular nature may facilitate therapeutic intervention in these conditions.
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Affiliation(s)
- Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore.
| | - David A Calderwood
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
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32
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Bademosi AT, Meunier FA. Unveiling the Nanoscale Dynamics of the Exocytic Machinery in Chromaffin Cells with Single-Molecule Imaging. Methods Mol Biol 2023; 2565:311-327. [PMID: 36205903 DOI: 10.1007/978-1-0716-2671-9_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Neuronal and hormonal communication relies on the exocytic fusion of vesicles containing neurotransmitters and hormones with the plasma membrane. This process is tightly regulated by key protein-protein and protein-lipid interactions and culminates in the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex formation and zippering that promotes vesicular fusion. Located on both sides of the vesicle and the plasma membrane, the zippering of the SNARE complex acts to overcome the energy barrier afforded by the repulsive electrostatic force stemming from apposing two negatively charged phospholipid membranes. Another component opposing the timely organization of the fusion machinery is thermal Brownian energy that tends to homogenize all cellular molecules by constantly switching their motions and directions through short-lived molecular interactions. Much less is known of the mechanisms counteracting these chaotic forces, allowing seamless cellular functions such as exocytic fusion. Super-resolution microscopy techniques such as single-molecule imaging have proven useful to start uncovering these nanoscale mechanisms. Here, we used single-particle tracking photoactivatable localization microscopy (sptPALM) to track syntaxin-1-mEos, a SNARE protein located on the plasma membrane of cultured bovine chromaffin cells. We demonstrate that syntaxin-1-mEos undergoes dramatic change in its mobility in response to secretagogue stimulation leading to increased nanoclustering. These nanoclusters are transient in nature and likely to provide docked vesicles with a molecular environment conducive to exocytic fusion.
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Affiliation(s)
- Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, St Lucia Campus, Brisbane, QLD, Australia.
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, St Lucia Campus, Brisbane, QLD, Australia.
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33
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GLUT4 translocation and dispersal operate in multiple cell types and are negatively correlated with cell size in adipocytes. Sci Rep 2022; 12:20535. [PMID: 36446811 PMCID: PMC9708847 DOI: 10.1038/s41598-022-24736-y] [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: 08/08/2022] [Accepted: 11/18/2022] [Indexed: 11/30/2022] Open
Abstract
The regulated translocation of the glucose transporter, GLUT4, to the surface of adipocytes and muscle is a key action of insulin. This is underpinned by the delivery and fusion of GLUT4-containing vesicles with the plasma membrane. Recent studies have revealed that a further action of insulin is to mediate the dispersal of GLUT4 molecules away from the site of GLUT4 vesicle fusion with the plasma membrane. Although shown in adipocytes, whether insulin-stimulated dispersal occurs in other cells and/or is exhibited by other proteins remains a matter of debate. Here we show that insulin stimulates GLUT4 dispersal in the plasma membrane of adipocytes, induced pluripotent stem cell-derived cardiomyocytes and HeLa cells, suggesting that this phenomenon is specific to GLUT4 expressed in all cell types. By contrast, insulin-stimulated dispersal of TfR was not observed in HeLa cells, suggesting that the mechanism may be unique to GLUT4. Consistent with dispersal being an important physiological mechanism, we observed that insulin-stimulated GLUT4 dispersal is reduced under conditions of insulin resistance. Adipocytes of different sizes have been shown to exhibit distinct metabolic properties: larger adipocytes exhibit reduced insulin-stimulated glucose transport compared to smaller cells. Here we show that both GLUT4 delivery to the plasma membrane and GLUT4 dispersal are reduced in larger adipocytes, supporting the hypothesis that larger adipocytes are refractory to insulin challenge compared to their smaller counterparts, even within a supposedly homogeneous population of cells.
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34
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Vanoli V, Delleani S, Casalegno M, Pizzetti F, Makvandi P, Haugen H, Mele A, Rossi F, Castiglione F. Hyaluronic acid-based hydrogels: Drug diffusion investigated by HR-MAS NMR and release kinetics. Carbohydr Polym 2022; 301:120309. [DOI: 10.1016/j.carbpol.2022.120309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/17/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022]
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35
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Liu X, Jiang Y, Cui Y, Yuan J, Fang X. Deep learning in single-molecule imaging and analysis: recent advances and prospects. Chem Sci 2022; 13:11964-11980. [PMID: 36349113 PMCID: PMC9600384 DOI: 10.1039/d2sc02443h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/19/2022] [Indexed: 09/19/2023] Open
Abstract
Single-molecule microscopy is advantageous in characterizing heterogeneous dynamics at the molecular level. However, there are several challenges that currently hinder the wide application of single molecule imaging in bio-chemical studies, including how to perform single-molecule measurements efficiently with minimal run-to-run variations, how to analyze weak single-molecule signals efficiently and accurately without the influence of human bias, and how to extract complete information about dynamics of interest from single-molecule data. As a new class of computer algorithms that simulate the human brain to extract data features, deep learning networks excel in task parallelism and model generalization, and are well-suited for handling nonlinear functions and extracting weak features, which provide a promising approach for single-molecule experiment automation and data processing. In this perspective, we will highlight recent advances in the application of deep learning to single-molecule studies, discuss how deep learning has been used to address the challenges in the field as well as the pitfalls of existing applications, and outline the directions for future development.
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Affiliation(s)
- Xiaolong Liu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yifei Jiang
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences Hangzhou 310022 Zhejiang China
| | - Yutong Cui
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Jinghe Yuan
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Xiaohong Fang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences Hangzhou 310022 Zhejiang China
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36
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Ng WS, Sielaff H, Zhao ZW. Phase Separation-Mediated Chromatin Organization and Dynamics: From Imaging-Based Quantitative Characterizations to Functional Implications. Int J Mol Sci 2022; 23:ijms23148039. [PMID: 35887384 PMCID: PMC9316379 DOI: 10.3390/ijms23148039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022] Open
Abstract
As an effective and versatile strategy to compartmentalize cellular components without the need for lipid membranes, phase separation has been found to underpin a wide range of intranuclear processes, particularly those involving chromatin. Many of the unique physico-chemical properties of chromatin-based phase condensates are harnessed by the cell to accomplish complex regulatory functions in a spatially and temporally controlled manner. Here, we survey key recent findings on the mechanistic roles of phase separation in regulating the organization and dynamics of chromatin-based molecular processes across length scales, packing states and intranuclear functions, with a particular emphasis on quantitative characterizations of these condensates enabled by advanced imaging-based approaches. By illuminating the complex interplay between chromatin and various chromatin-interacting molecular species mediated by phase separation, this review sheds light on an emerging multi-scale, multi-modal and multi-faceted landscape that hierarchically regulates the genome within the highly crowded and dynamic nuclear space. Moreover, deficiencies in existing studies also highlight the need for mechanism-specific criteria and multi-parametric approaches for the characterization of chromatin-based phase separation using complementary techniques and call for greater efforts to correlate the quantitative features of these condensates with their functional consequences in close-to-native cellular contexts.
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Affiliation(s)
- Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411, Singapore
- Correspondence:
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37
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Zhang MQ, Wang ZG, Fu DD, Zhang JM, Liu HY, Liu SL, Pang DW. Quantum Dots Tracking Endocytosis and Transport of Proteins Displayed by Mammalian Cells. Anal Chem 2022; 94:7567-7575. [PMID: 35581735 DOI: 10.1021/acs.analchem.2c00411] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mammalian cell display technology uses eukaryotic protein expression system to display proteins on cell surfaces and has become an important method in biological research. Although mammalian cell display technology has many advantages and development potential, certain attributes of the displayed protein remain uncharacterized, such as whether the displayed proteins re-enter the cell and how displayed proteins move into the cell. Here, we present the endocytosis mechanism, motility behavior, and transport kinetics of displayed proteins determined using HaloTag as the displayed protein and quantum dot-based single-particle tracking. The displayed protein enters the cell through clathrin-mediated endocytosis and is transported through the cell in three stages, which is dependent on microfilaments and microtubules. The dynamic information obtained in this study provides answers to questions about endocytosis and postendocytosis transport of displayed proteins and, therefore, is expected to facilitate the development of surface display technology.
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Affiliation(s)
- Meng-Qian Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Dan-Dan Fu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Ju-Mei Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Hao-Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Dai-Wen Pang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, and School of Medicine, Nankai University, Tianjin 300071, P. R. China
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38
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Spatiotemporal stop-and-go dynamics of the mitochondrial TOM core complex correlates with channel activity. Commun Biol 2022; 5:471. [PMID: 35581327 PMCID: PMC9114391 DOI: 10.1038/s42003-022-03419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/26/2022] [Indexed: 11/08/2022] Open
Abstract
Single-molecule studies can reveal phenomena that remain hidden in ensemble measurements. Here we show the correlation between lateral protein diffusion and channel activity of the general protein import pore of mitochondria (TOM-CC) in membranes resting on ultrathin hydrogel films. Using electrode-free optical recordings of ion flux, we find that TOM-CC switches reversibly between three states of ion permeability associated with protein diffusion. While freely diffusing TOM-CC molecules are predominantly in a high permeability state, non-mobile molecules are mostly in an intermediate or low permeability state. We explain this behavior by the mechanical binding of the two protruding Tom22 subunits to the hydrogel and a concomitant combinatorial opening and closing of the two β-barrel pores of TOM-CC. TOM-CC could thus represent a β-barrel membrane protein complex to exhibit membrane state-dependent mechanosensitive properties, mediated by its two Tom22 subunits.
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39
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Boruah A, Saikia BK. Synthesis, Characterization, Properties, and Novel Applications of Fluorescent Nanodiamonds. J Fluoresc 2022; 32:863-885. [PMID: 35230567 DOI: 10.1007/s10895-022-02898-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
Abstract
In the last few years, fluorescent nanodiamonds (FNDs) have been developed significantly as a new member in the nanocarbon family. The surface of FNDs is embedded with some crystallographic defects containing color centres which surmount the properties of other fluorochromes including up conversion and down conversion nanoparticles, quantum dots, nano tubes, fullerenes, organic dyes, silica etc. Some of the intriguing properties like inevitable photostability, inherent bio-compatibility, outstanding optical and robust mechanical properties, excellent magnetic field, and electric field sensing potentiality make FNDs appealing to some benevolent applications in numerous fields like bio-imaging, delivering drugs, fighting cancer, spin electronics, imaging of magnetic structure at nanoscale and as promising nanometric temperature sensor. The structure of FNDs has certain point defects on the surface among which negatively charged nitrogen vacancy centre (NV-) is the most investigated color centre. The production of NV- fluorescence nanodiamonds is the most challenging task as substitution of carbon atoms is required to create vacancies by causing irradiation from an electron beam which is followed by high temperature annealing. Thus, this review points out the relative advantages of FNDs containing negatively charged nitrogen vacancy centres produced from HPHT method or CVD method with those nanodiamonds produced through detonation process or pulsed laser ablation (PLA) method. The steps involved in the fabrication of FNDs are described along with the major challenges and struggles underwent during the process in this review. This review also summarizes the recent developments made in the functionalization and applications predominantly made in the field of biological science and it is understood that depending on the defect color centres they can exhibit different emitted wavelengths ranging from UV-visible to near infrared with broad or narrow bandwidths. This review also highlights some of the fluorescent NDs that emit stable and strong red or green photoluminescence from the defect centers of NV- which are implanted in the crystal lattice. This critical and extensive review will be useful for the further progress in this futuristic field of FNDs.
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Affiliation(s)
- Anusuya Boruah
- Coal & Energy Group, Materials Science and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Binoy K Saikia
- Coal & Energy Group, Materials Science and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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Sotolongo Bellón J, Birkholz O, Richter CP, Eull F, Kenneweg H, Wilmes S, Rothbauer U, You C, Walter MR, Kurre R, Piehler J. Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane. CELL REPORTS METHODS 2022; 2:100165. [PMID: 35474965 PMCID: PMC9017138 DOI: 10.1016/j.crmeth.2022.100165] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
Abstract
Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
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Affiliation(s)
- Junel Sotolongo Bellón
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Christian P. Richter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Florian Eull
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Hella Kenneweg
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
- Division of Cell Signalling and Immunology, University of Dundee, School of Life Sciences, Dundee, UK
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls-University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rainer Kurre
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
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Yoshimura H. Triple-color single-molecule imaging for analysis of the role of receptor oligomers in signal transduction. Biophys Physicobiol 2022; 19:1-9. [PMID: 35435651 PMCID: PMC8968032 DOI: 10.2142/biophysico.bppb-v19.0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 12/01/2022] Open
Abstract
Membrane receptors provide interfaces of various extracellular stimuli to transduce the signal into the cell. Receptors are required to possess such conflicting properties as high sensitivity and noise reduction for the cell to keep its homeostasis and appropriate responses. To understand the mechanisms by which these functions are achieved, single-molecule monitoring of the motilities of receptors and signaling molecules on the plasma membrane is one of the most direct approaches. This review article introduces several recent single-molecule imaging studies of receptors, including the author’s recent work on triple-color single-molecule imaging of G protein-coupled receptors. Based on these researches, advantages and perspectives of the single-molecule imaging approach to solving the mechanisms of receptor functions are illustrated.
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Tomlinson ID, Kovtun O, Torres R, Bellocchio LG, Josephs T, Rosenthal SJ. A Novel Biotinylated Homotryptamine Derivative for Quantum Dot Imaging of Serotonin Transporter in Live Cells. Front Cell Neurosci 2021; 15:667044. [PMID: 34867196 PMCID: PMC8637195 DOI: 10.3389/fncel.2021.667044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/19/2021] [Indexed: 11/21/2022] Open
Abstract
The serotonin transporter (SERT) is the primary target for selective serotonin reuptake inhibitor (SSRI) antidepressants that are thought to exert their therapeutic effects by increasing the synaptic concentration of serotonin. Consequently, probes that can be utilized to study cellular trafficking of SERT are valuable research tools. We have developed a novel ligand (IDT785) that is composed of a SERT antagonist (a tetrahydro pyridyl indole derivative) conjugated to a biotinylated poly ethylene glycol (PEG) via a phenethyl linker. This compound was determined to be biologically active and inhibited SERT-mediated reuptake of IDT307 with the half-maximal inhibitory concentration of 7.2 ± 0.3 μM. We demonstrated that IDT785 enabled quantum dot (QD) labeling of membrane SERT in transfected HEK-293 cultures that could be blocked using the high affinity serotonin reuptake inhibitor paroxetine. Molecular docking studies suggested that IDT785 might be binding to the extracellular vestibule binding site rather than the orthosteric substrate binding site, which could be attributable to the hydrophilicity of the PEG chain and the increased loss of degrees of freedom that would be required to penetrate into the orthosteric binding site. Using IDT785, we were able to study the membrane localization and membrane dynamics of YFP-SERT heterologously expressed in HEK-293 cells and demonstrated that SERT expression was enriched in the membrane edge and in thin cellular protrusions.
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Affiliation(s)
- Ian D. Tomlinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Oleg Kovtun
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Ruben Torres
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Travis Josephs
- Neuroscience Program, Vanderbilt University, Nashville, TN, United States
| | - Sandra J. Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN, United States
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Podh NK, Paliwal S, Dey P, Das A, Morjaria S, Mehta G. In-vivo Single-Molecule Imaging in Yeast: Applications and Challenges. J Mol Biol 2021; 433:167250. [PMID: 34537238 DOI: 10.1016/j.jmb.2021.167250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Single-molecule imaging has gained momentum to quantify the dynamics of biomolecules in live cells, as it provides direct real-time measurements of various cellular activities under their physiological environment. Yeast, a simple and widely used eukaryote, serves as a good model system to quantify single-molecule dynamics of various cellular processes because of its low genomic and cellular complexities, as well as its facile ability to be genetically manipulated. In the past decade, significant developments have been made regarding the intracellular labeling of biomolecules (proteins, mRNA, fatty acids), the microscopy setups to visualize single-molecules and capture their fast dynamics, and the data analysis pipelines to interpret such dynamics. In this review, we summarize the current state of knowledge for the single-molecule imaging in live yeast cells to provide a ready reference for beginners. We provide a comprehensive table to demonstrate how various labs tailored the imaging regimes and data analysis pipelines to estimate various biophysical parameters for a variety of biological processes. Lastly, we present current challenges and future directions for developing better tools and resources for single-molecule imaging in live yeast cells.
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Affiliation(s)
- Nitesh Kumar Podh
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@PodhNitesh
| | - Sheetal Paliwal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@Sheetal62666036
| | - Partha Dey
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@ParthaD63416958
| | - Ayan Das
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India. https://twitter.com/@AyanDas76471821
| | - Shruti Morjaria
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India. https://twitter.com/@shruti_morjaria
| | - Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India.
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Godó S, Barabás K, Lengyel F, Ernszt D, Kovács T, Kecskés M, Varga C, Jánosi TZ, Makkai G, Kovács G, Orsolits B, Fujiwara T, Kusumi A, Ábrahám IM. Single-Molecule Imaging Reveals Rapid Estradiol Action on the Surface Movement of AMPA Receptors in Live Neurons. Front Cell Dev Biol 2021; 9:708715. [PMID: 34631701 PMCID: PMC8495425 DOI: 10.3389/fcell.2021.708715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/07/2021] [Indexed: 01/04/2023] Open
Abstract
Gonadal steroid 17β-estradiol (E2) exerts rapid, non-genomic effects on neurons and strictly regulates learning and memory through altering glutamatergic neurotransmission and synaptic plasticity. However, its non-genomic effects on AMPARs are not well understood. Here, we analyzed the rapid effect of E2 on AMPARs using single-molecule tracking and super-resolution imaging techniques. We found that E2 rapidly decreased the surface movement of AMPAR via membrane G protein-coupled estrogen receptor 1 (GPER1) in neurites in a dose-dependent manner. The cortical actin network played a pivotal role in the GPER1 mediated effects of E2 on the surface mobility of AMPAR. E2 also decreased the surface movement of AMPAR both in synaptic and extrasynaptic regions on neurites and increased the synaptic dwell time of AMPARs. Our results provide evidence for understanding E2 action on neuronal plasticity and glutamatergic neurotransmission at the molecular level.
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Affiliation(s)
- Soma Godó
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Klaudia Barabás
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Ferenc Lengyel
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Dávid Ernszt
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Tamás Kovács
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Miklós Kecskés
- PTE-NAP Cortical Microcircuits Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, Pécs, Hungary
| | - Csaba Varga
- PTE-NAP Cortical Microcircuits Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, Pécs, Hungary
| | - Tibor Z Jánosi
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Géza Makkai
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Gergely Kovács
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
| | - Barbara Orsolits
- Laboratory of Neuroimmunology, Institute of Experimental Medicine of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Akihiro Kusumi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Onna, Japan
| | - István M Ábrahám
- PTE-NAP Molecular Neuroendocrinology Research Group, Centre for Neuroscience, Szentágothai Research Center, Medical School, Institute of Physiology, University of Pécs, Pécs, Hungary
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45
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Chen X, Liu T, Qin X, Nguyen QQ, Lee SK, Lee C, Ren Y, Chu J, Zhu G, Yoon TY, Park CY, Park H. Simultaneous Real-Time Three-Dimensional Localization and FRET Measurement of Two Distinct Particles. NANO LETTERS 2021; 21:7479-7485. [PMID: 34491760 DOI: 10.1021/acs.nanolett.1c01328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological processes employ mechanisms involving the locations and interactions of multiple components. Given that most biological processes occur in three dimensions, the simultaneous measurement of three-dimensional locations and interactions is necessary. However, the simultaneous three-dimensional precise localization and measurement of interactions in real time remains challenging. Here, we report a new microscopy technique to localize two spectrally distinct particles in three dimensions with an accuracy (2.35σ) of tens of nanometers with an exposure time of 100 ms and to measure their real-time interactions using fluorescence resonance energy transfer (FRET) simultaneously. Using this microscope, we tracked two distinct vesicles containing t-SNAREs or v-SNARE in three dimensions and observed FRET simultaneously during single-vesicle fusion in real time, revealing the nanoscale motion and interactions of single vesicles in vesicle fusion. Thus, this study demonstrates that our microscope can provide detailed information about real-time three-dimensional nanoscale locations, motion, and interactions in biological processes.
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Affiliation(s)
- Xingxiang Chen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Quang Quan Nguyen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Chanwoo Lee
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Yaguang Ren
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tae-Young Yoon
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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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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Kim M, Hong S, Yankeelov TE, Yeh HC, Liu YL. Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics. Bioinformatics 2021; 38:243-249. [PMID: 34390568 PMCID: PMC8696113 DOI: 10.1093/bioinformatics/btab581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/09/2021] [Accepted: 08/12/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Motions of transmembrane receptors on cancer cell surfaces can reveal biophysical features of the cancer cells, thus providing a method for characterizing cancer cell phenotypes. While conventional analysis of receptor motions in the cell membrane mostly relies on the mean-squared displacement plots, much information is lost when producing these plots from the trajectories. Here we employ deep learning to classify breast cancer cell types based on the trajectories of epidermal growth factor receptor (EGFR). Our model is an artificial neural network trained on the EGFR motions acquired from six breast cancer cell lines of varying invasiveness and receptor status: MCF7 (hormone receptor positive), BT474 (HER2-positive), SKBR3 (HER2-positive), MDA-MB-468 (triple negative, TN), MDA-MB-231 (TN) and BT549 (TN). RESULTS The model successfully classified the trajectories within individual cell lines with 83% accuracy and predicted receptor status with 85% accuracy. To further validate the method, epithelial-mesenchymal transition (EMT) was induced in benign MCF10A cells, noninvasive MCF7 cancer cells and highly invasive MDA-MB-231 cancer cells, and EGFR trajectories from these cells were tested. As expected, after EMT induction, both MCF10A and MCF7 cells showed higher rates of classification as TN cells, but not the MDA-MB-231 cells. Whereas deep learning-based cancer cell classifications are primarily based on the optical transmission images of cell morphology and the fluorescence images of cell organelles or cytoskeletal structures, here we demonstrated an alternative way to classify cancer cells using a dynamic, biophysical feature that is readily accessible. AVAILABILITY AND IMPLEMENTATION A python implementation of deep learning-based classification can be found at https://github.com/soonwoohong/Deep-learning-for-EGFR-trajectory-classification. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Thomas E Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712, USA,Oden Institute for Computational Engineering and Science, The University of Texas at Austin, TX 78712, USA,Department of Diagnostic Medicine, The University of Texas at Austin, TX 78712, USA,Department of Oncology, The University of Texas at Austin, TX 78712, USA,Livestrong Cancer Institutes, The University of Texas at Austin, TX 78712, USA
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48
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Kovtun O, Torres R, Bellocchio LG, Rosenthal SJ. Membrane Nanoscopic Organization of D2L Dopamine Receptor Probed by Quantum Dot Tracking. MEMBRANES 2021; 11:578. [PMID: 34436341 PMCID: PMC8401772 DOI: 10.3390/membranes11080578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/11/2023]
Abstract
The role of lateral mobility and nanodomain organization of G protein-coupled receptors in modulating subcellular signaling has been under increasing scrutiny. Investigation of D2 dopamine receptor diffusion dynamics is of particular interest, as these receptors have been linked to altered neurotransmission in affective disorders and represent the primary target for commonly prescribed antipsychotics. Here, we applied our single quantum dot tracking approach to decipher intrinsic diffusion patterns of the wild-type long isoform of the D2 dopamine receptor and its genetic variants previously identified in several cohorts of schizophrenia patients. We identified a subtle decrease in the diffusion rate of the Val96Ala mutant that parallels its previously reported reduced affinity for potent neuroleptics clozapine and chlorpromazine. Slower Val96Ala variant diffusion was not accompanied by a change in receptor-receptor transient interactions as defined by the diffraction-limited quantum dot colocalization events. In addition, we implemented a Voronoї tessellation-based algorithm to compare nanoclustering of the D2 dopamine receptor to the dominant anionic phospholipid phosphatidylinositol 4,5-bisphosphate in the plasma membrane of live cells.
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Affiliation(s)
- Oleg Kovtun
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
| | - Ruben Torres
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Laurel G. Bellocchio
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
| | - Sandra Jean Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; (R.T.); (L.G.B.)
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN 37235, USA
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Ma L, Geng J, Kolossov VL, Han Z, Pei Y, Lim SJ, Kilian KA, Smith AM. Antibody Self-Assembly Maximizes Cytoplasmic Immunostaining Accuracy of Compact Quantum Dots. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:4877-4889. [PMID: 35221487 PMCID: PMC8880911 DOI: 10.1021/acs.chemmater.1c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antibody conjugates of quantum dots (QDs) are expected to transform immunofluorescence staining by expanding multiplexed analysis and improving target quantification. Recently, a new generation of small QDs coated with multidentate polymers has improved QD labeling density in diverse biospecimens, but new challenges prevent their routine use. In particular, these QDs exhibit nonspecific binding to fixed cell nuclei and their antibody conjugates have random attachment orientations. This report describes four high-efficiency chemical approaches to conjugate antibodies to compact QDs. Methods include click chemistry and self-assembly through polyhistidine coordination, both with and without adaptor proteins that directionally orient antibodies. Specific and nonspecific labeling are independently analyzed after application of diverse blocking agent classes, and a new assay is developed to quantitatively measure intracellular labeling density based on microtubule stain connectivity. Results show that protein conjugation to the QD surface is required to simultaneously eliminate nonspecific binding and maintain antigen specificity. Of the four conjugation schemes, polyhistidine-based coordination of adaptor proteins with antibody self-assembly yields the highest intracellular staining density and the simplest conjugation procedure. Therefore, antibody and adaptor protein orientation, in addition to blocking optimization, are important determinants of labeling outcomes, insights that can inform translational development of these more compact nanomaterials.
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Affiliation(s)
- Liang Ma
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junlong Geng
- Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vladimir L Kolossov
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhiyuan Han
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Pei
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sung Jun Lim
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Division of Nanotechnology, Dalseong-Gun 42988, Republic of Korea
| | - Kristopher A Kilian
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; School of Materials Science and Engineering and School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Andrew M Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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Nanopore-mediated protein delivery enabling three-color single-molecule tracking in living cells. Proc Natl Acad Sci U S A 2021; 118:2012229118. [PMID: 33495347 DOI: 10.1073/pnas.2012229118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Multicolor single-molecule tracking (SMT) provides a powerful tool to mechanistically probe molecular interactions in living cells. However, because of the limitations in the optical and chemical properties of currently available fluorophores and the multiprotein labeling strategies, intracellular multicolor SMT remains challenging for general research studies. Here, we introduce a practical method employing a nanopore-electroporation (NanoEP) technique to deliver multiple organic dye-labeled proteins into living cells for imaging. It can be easily expanded to three channels in commercial microscopes or be combined with other in situ labeling methods. Utilizing NanoEP, we demonstrate three-color SMT for both cytosolic and membrane proteins. Specifically, we simultaneously monitored single-molecule events downstream of EGFR signaling pathways in living cells. The results provide detailed resolution of the spatial localization and dynamics of Grb2 and SOS recruitment to activated EGFR along with the resultant Ras activation.
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