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Presman DM, Benítez B, Lafuente AL, Vázquez Lareu A. Chromatin structure and dynamics: one nucleosome at a time. Histochem Cell Biol 2024; 162:79-90. [PMID: 38607419 DOI: 10.1007/s00418-024-02281-1] [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] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Eukaryotic genomes store information on many levels, including their linear DNA sequence, the posttranslational modifications of its constituents (epigenetic modifications), and its three-dimensional folding. Understanding how this information is stored and read requires multidisciplinary collaborations from many branches of science beyond biology, including physics, chemistry, and computer science. Concurrent recent developments in all these areas have enabled researchers to image the genome with unprecedented spatial and temporal resolution. In this review, we focus on what single-molecule imaging and tracking of individual proteins in live cells have taught us about chromatin structure and dynamics. Starting with the basics of single-molecule tracking (SMT), we describe some advantages over in situ imaging techniques and its current limitations. Next, we focus on single-nucleosome studies and what they have added to our current understanding of the relationship between chromatin dynamics and transcription. In celebration of Robert Feulgen's ground-breaking discovery that allowed us to start seeing the genome, we discuss current models of chromatin structure and future challenges ahead.
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Affiliation(s)
- Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina.
| | - Belén Benítez
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Agustina L Lafuente
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
| | - Alejo Vázquez Lareu
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
- Instituto de Química Biológica (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, C1428EGA, Buenos Aires, Argentina
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2
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Brenner B, Sun C, Raymo FM, Zhang HF. Spectroscopic single-molecule localization microscopy: applications and prospective. NANO CONVERGENCE 2023; 10:14. [PMID: 36943541 PMCID: PMC10030755 DOI: 10.1186/s40580-023-00363-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/05/2023] [Indexed: 05/25/2023]
Abstract
Single-molecule localization microscopy (SMLM) breaks the optical diffraction limit by numerically localizing sparse fluorescence emitters to achieve super-resolution imaging. Spectroscopic SMLM or sSMLM further allows simultaneous spectroscopy and super-resolution imaging of fluorescence molecules. Hence, sSMLM can extract spectral features with single-molecule sensitivity, higher precision, and higher multiplexity than traditional multicolor microscopy modalities. These new capabilities enabled advanced multiplexed and functional cellular imaging applications. While sSMLM suffers from reduced spatial precision compared to conventional SMLM due to splitting photons to form spatial and spectral images, several methods have been reported to mitigate these weaknesses through innovative optical design and image processing techniques. This review summarizes the recent progress in sSMLM, its applications, and our perspective on future work.
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Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Françisco M Raymo
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
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3
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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4
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Matsumori H, Watanabe K, Tachiwana H, Fujita T, Ito Y, Tokunaga M, Sakata-Sogawa K, Osakada H, Haraguchi T, Awazu A, Ochiai H, Sakata Y, Ochiai K, Toki T, Ito E, Goldberg IG, Tokunaga K, Nakao M, Saitoh N. Ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly. Life Sci Alliance 2022; 5:5/7/e202101045. [PMID: 35321919 PMCID: PMC8942980 DOI: 10.26508/lsa.202101045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
High content image analysis, single molecule tracking, modeling, and DBA patient analysis revealed that ribosomal protein L5 facilitates rDNA-bundled condensate and nucleolar assembly. The nucleolus is the site of ribosome assembly and formed through liquid–liquid phase separation. Multiple ribosomal DNA (rDNA) arrays are bundled in the nucleolus, but the underlying mechanism and significance are unknown. In the present study, we performed high-content screening followed by image profiling with the wndchrm machine learning algorithm. We revealed that cells lacking a specific 60S ribosomal protein set exhibited common nucleolar disintegration. The depletion of RPL5 (also known as uL18), the liquid–liquid phase separation facilitator, was most effective, and resulted in an enlarged and un-separated sub-nucleolar compartment. Single-molecule tracking analysis revealed less-constrained mobility of its components. rDNA arrays were also unbundled. These results were recapitulated by a coarse-grained molecular dynamics model. Transcription and processing of ribosomal RNA were repressed in these aberrant nucleoli. Consistently, the nucleoli were disordered in peripheral blood cells from a Diamond–Blackfan anemia patient harboring a heterozygous, large deletion in RPL5. Our combinatorial analyses newly define the role of RPL5 in rDNA array bundling and the biophysical properties of the nucleolus, which may contribute to the etiology of ribosomopathy.
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Affiliation(s)
- Haruka Matsumori
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Kenji Watanabe
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiroaki Tachiwana
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomoko Fujita
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kumiko Sakata-Sogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, Japan.,Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuka Sakata
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Ilya G Goldberg
- Image Informatics and Computational Biology Unit, Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kazuaki Tokunaga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Noriko Saitoh
- Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
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5
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Uchino S, Ito Y, Sato Y, Handa T, Ohkawa Y, Tokunaga M, Kimura H. Live imaging of transcription sites using an elongating RNA polymerase II-specific probe. J Cell Biol 2022; 221:212888. [PMID: 34854870 PMCID: PMC8647360 DOI: 10.1083/jcb.202104134] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/12/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In eukaryotic nuclei, most genes are transcribed by RNA polymerase II (RNAP2), whose regulation is a key to understanding the genome and cell function. RNAP2 has a long heptapeptide repeat (Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7), and Ser2 is phosphorylated on an elongation form. To detect RNAP2 Ser2 phosphorylation (RNAP2 Ser2ph) in living cells, we developed a genetically encoded modification-specific intracellular antibody (mintbody) probe. The RNAP2 Ser2ph-mintbody exhibited numerous foci, possibly representing transcription “factories,” and foci were diminished during mitosis and in a Ser2 kinase inhibitor. An in vitro binding assay using phosphopeptides confirmed the mintbody’s specificity. RNAP2 Ser2ph-mintbody foci were colocalized with proteins associated with elongating RNAP2 compared with factors involved in the initiation. These results support the view that mintbody localization represents the sites of RNAP2 Ser2ph in living cells. RNAP2 Ser2ph-mintbody foci showed constrained diffusional motion like chromatin, but they were more mobile than DNA replication domains and p300-enriched foci, suggesting that the elongating RNAP2 complexes are separated from more confined chromatin domains.
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Affiliation(s)
- Satoshi Uchino
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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6
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Cao F, Li Y, Wu J, Liu W, Ngai T. Measurements of interactions between fluorescent molecules and polyethylene glycol self-assembled monolayers. SOFT MATTER 2021; 18:236-243. [PMID: 34874390 DOI: 10.1039/d1sm01329g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Blocking the non-specific binding of fluorescent biomolecules to substrates is one of the most important approaches to minimize the background noise in single-molecule fluorescence detection. Polyethylene glycol (PEG) and its derivatives are the most frequently used self-assembled monolayers (SAMs) for surface passivation because they are particularly effective to reduce the adsorption of a majority of biomolecules. Most studies related to PEG SAMs focus only on the interactions between biomolecules and substrates, while few reports exist in which the interactions between fluorophores and organosilane SAMs are directly examined. The objective of this study is to try to clarify the interactions between fluorescein isothiocyanate (FITC) and PEG SAMs at different ionic strengths. Total internal reflection microscopy (TIRM) was utilized for quantitative analysis of the interactions. At low ionic strength, long-range attractions between FITC-modified polystyrene-silica particles and PEG SAM grafting substrates were observed, even though both of them had an ensemble-averaged negative charge. The origin of this attraction could be correlated to their nonuniformly charged surfaces. At high ionic strength, van der Waals attraction at short distances was measured as the electrostatic interactions were completely screened. Due to the polarizability of the FITC molecule, the van der Waals attractions increased with the thickness of the PEG SAMs. This phenomenon is explained by the hydration shell of the PEG SAMs.
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Affiliation(s)
- Feng Cao
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - Yinan Li
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - Jiahao Wu
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - Wei Liu
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - To Ngai
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
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7
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Brenner B, Song KH, Sun C, Zhang HF. Improving spatial precision and field-of-view in wavelength-tagged single-particle tracking using spectroscopic single-molecule localization microscopy. APPLIED OPTICS 2021; 60:3647-3658. [PMID: 33983297 PMCID: PMC8648066 DOI: 10.1364/ao.415275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/30/2021] [Indexed: 05/09/2023]
Abstract
Spectroscopic single-molecule localization microscopy (sSMLM) generates super-resolution images of single molecules while simultaneously capturing the spectra of their fluorescence emissions. However, sSMLM splits photons from single-molecule emissions into a spatial channel and a spectral channel, reducing both channels' precisions. It is also challenging in transmission grating-based sSMLM to achieve a large field-of-view (FOV) and avoid overlap between the spatial and spectral channels. The challenge in FOV has further significance in single-molecule tracking applications. In this work, we analyzed the correlation between the spatial and spectral channels in sSMLM to improve its spatial precision, and we developed a split-mirror assembly to enlarge its FOV. We demonstrate the benefits of these improvements by tracking quantum dots. We also show that we can reduce particle-identification ambiguity by tagging each particle with its unique spectral characteristics.
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Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
| | - Ki-Hee Song
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
| | - Hao F. Zhang
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA
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8
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Ito Y, Kimura A. Session 1SEA-physics of chromatin dynamics at the 57th Biophysical Society of Japan meeting. Biophys Rev 2020; 12:265-266. [PMID: 32056110 DOI: 10.1007/s12551-020-00642-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/06/2020] [Indexed: 01/07/2023] Open
Affiliation(s)
- Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori, Yokohama, 226-8501, Japan
| | - Akatsuki Kimura
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima, 411-8540, Japan. .,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima, 411-8540, Japan.
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9
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Lee Y, Phelps C, Huang T, Mostofian B, Wu L, Zhang Y, Tao K, Chang YH, Stork PJ, Gray JW, Zuckerman DM, Nan X. High-throughput, single-particle tracking reveals nested membrane domains that dictate KRas G12D diffusion and trafficking. eLife 2019; 8:46393. [PMID: 31674905 PMCID: PMC7060040 DOI: 10.7554/elife.46393] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Membrane nanodomains have been implicated in Ras signaling, but what these domains are and how they interact with Ras remain obscure. Here, using single particle tracking with photoactivated localization microscopy (spt-PALM) and detailed trajectory analysis, we show that distinct membrane domains dictate KRasG12D (an active KRas mutant) diffusion and trafficking in U2OS cells. KRasG12D exhibits an immobile state in ~70 nm domains, each embedded in a larger domain (~200 nm) that confers intermediate mobility, while the rest of the membrane supports fast diffusion. Moreover, KRasG12D is continuously removed from the membrane via the immobile state and replenished to the fast state, reminiscent of Ras internalization and recycling. Importantly, both the diffusion and trafficking properties of KRasG12D remain invariant over a broad range of protein expression levels. Our results reveal how membrane organization dictates membrane diffusion and trafficking of Ras and offer new insight into the spatial regulation of Ras signaling. The Ras family of proteins play an important role in relaying signals from the outside to the inside of the cell. Ras proteins are attached by a fatty tail to the inner surface of the cell membrane. When activated they transmit a burst of signal that controls critical behaviors like growth, survival and movement. It has been suggested that to prevent these signals from being accidently activated, Ras molecules must group together at specialized sites within the membrane before passing on their message. However, visualizing how Ras molecules cluster together at these domains has thus far been challenging. As a result, little is known about where these sites are located and how Ras molecules come to a stop at these domains. Now, Lee et al. have combined two microscopy techniques called ‘single-particle tracking’ and ‘photoactivated localization microscopy' to track how individual molecules of activated Ras move in human cells grown in the lab. This revealed that Ras molecules quickly diffuse along the inside of the membrane until they arrive at certain locations that cause them to halt. However, computer models consisting of just the ‘fast’ and ‘immobile’ state could not correctly re-capture the way Ras molecules moved along the membrane. Lee et al. found that for these models to mimic the movement of Ras, a third ‘intermediate’ state of Ras mobility needed to be included. To investigate this further, Lee et al. created a fluorescent map that overlaid all the individual paths taken by each Ras molecule. The map showed regions in the membrane where the Ras molecules had stopped and possibly clustered together. Each of these ‘immobilization domains’ were then surrounded by an ‘intermediate domain’ where Ras molecules had begun to slow down their movement. Although the intermediate domains did not last long, they seemed to guide Ras molecules into the immobilization domains where they could cluster together with other molecules. From there, the cell constantly removed Ras molecules from these membrane domains and returned them back to their ‘fast’ diffusing state. Mutations in Ras proteins occur in around a third of all cancers, so a better understanding of their dynamics could help with future drug discovery. The methods used here could also be used to investigate the movement of other signaling molecules.
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Affiliation(s)
- Yerim Lee
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Carey Phelps
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Barmak Mostofian
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Lei Wu
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Ying Zhang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Kai Tao
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Philip Js Stork
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Knight Cancer Early Detection Advanced Research (CEDAR) Center, Oregon Health and Science University, Portland, United States
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10
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Clarke DT, Martin-Fernandez ML. A Brief History of Single-Particle Tracking of the Epidermal Growth Factor Receptor. Methods Protoc 2019; 2:mps2010012. [PMID: 31164594 PMCID: PMC6481046 DOI: 10.3390/mps2010012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
Single-particle tracking (SPT) has been used and developed over the last 25 years as a method to investigate molecular dynamics, structure, interactions, and function in the cellular context. SPT is able to show how fast and how far individual molecules move, identify different dynamic populations, measure the duration and strength of intermolecular interactions, and map out structures on the nanoscale in cells. In combination with other techniques such as macromolecular crystallography and molecular dynamics simulation, it allows us to build models of complex structures, and develop and test hypotheses of how these complexes perform their biological roles in health as well as in disease states. Here, we use the example of the epidermal growth factor receptor (EGFR), which has been studied extensively by SPT, demonstrating how the method has been used to increase our understanding of the receptor’s organization and function, including its interaction with the plasma membrane, its activation, clustering, and oligomerization, and the role of other receptors and endocytosis. The examples shown demonstrate how SPT might be employed in the investigation of other biomolecules and systems.
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Affiliation(s)
- David T Clarke
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
| | - Marisa L Martin-Fernandez
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, UK.
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