1
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Nordahl L, Akkuratov EE, Heimgärtner J, Schach K, Meineke B, Elsässer S, Wennmalm S, Brismar H. Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS. Biochim Biophys Acta Gen Subj 2024; 1868:130619. [PMID: 38643888 DOI: 10.1016/j.bbagen.2024.130619] [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] [Received: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
The sodium potassium pump, Na,K-ATPase (NKA), is an integral plasma membrane protein, expressed in all eukaryotic cells. It is responsible for maintaining the transmembrane Na+ gradient and is the major determinant of the membrane potential. Self-interaction and oligomerization of NKA in cell membranes has been proposed and discussed but is still an open question. Here, we have used a combination of FRET and Fluorescence Correlation Spectroscopy, FRET-FCS, to analyze NKA in the plasma membrane of living cells. Click chemistry was used to conjugate the fluorescent labels Alexa 488 and Alexa 647 to non-canonical amino acids introduced in the NKA α1 and β1 subunits. We demonstrate that FRET-FCS can detect an order of magnitude lower concentration of green-red labeled protein pairs in a single-labeled red and green background than what is possible with cross-correlation (FCCS). We show that a significant fraction of NKA is expressed as a dimer in the plasma membrane. We also introduce a method to estimate not only the number of single and double labeled NKA, but the number of unlabeled, endogenous NKA and estimate the density of endogenous NKA at the plasma membrane to 1400 ± 800 enzymes/μm2.
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Affiliation(s)
- Linnea Nordahl
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden
| | - Evgeny E Akkuratov
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Johannes Heimgärtner
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Katja Schach
- Graduate Training Centre of Neuroscience, University of Tübingen, Otfried-Müller-Str. 27, 72076 Tübingen, Germany
| | - Birthe Meineke
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Simon Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
| | - Stefan Wennmalm
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden.
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, 171 21 Solna, Sweden; Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Box 1031, 171 21 Solna, Sweden
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2
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Sanaee M, Ronquist KG, Sandberg E, Morrell JM, Widengren J, Gallo K. Antibody-Loading of Biological Nanocarrier Vesicles Derived from Red-Blood-Cell Membranes. ACS OMEGA 2024; 9:22711-22718. [PMID: 38826552 PMCID: PMC11137724 DOI: 10.1021/acsomega.4c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 06/04/2024]
Abstract
Antibodies, disruptive potent therapeutic agents against pharmacological targets, face a barrier in crossing immune systems and cellular membranes. To overcome these, various strategies have been explored including shuttling via liposomes or biocamouflaged nanoparticles. Here, we demonstrate the feasibility of loading antibodies into exosome-mimetic nanovesicles derived from human red-blood-cell membranes, which can act as nanocarriers for intracellular delivery. Goat-antichicken antibodies are loaded into erythrocyte-derived nanovesicles, and their loading yields are characterized and compared with smaller dUTP-cargo molecules. Applying dual-color coincident fluorescence burst analyses, the loading yield of nanocarriers is rigorously profiled at the single-vesicle level, overcoming challenges due to size-heterogeneity and demonstrating a maximum antibody-loading yield of 38-41% at the optimal vesicle radius of 52 nm. The achieved average loading yields, amounting to 14% across the entire nanovesicle population, with more than two antibodies per loaded vesicle, are fully comparable to those obtained for the much smaller dUTP molecules loaded in the nanovesicles after additional exosome-spin-column purification. The results suggest a promising new avenue for therapeutic delivery of antibodies, potentially encompassing also intracellular targets and suitable for large-scale pharmacological applications, which relies on the exosome-mimetic properties, biocompatibility, and low-immunogenicity of bioengineered nanocarriers synthesized from human erythrocyte membranes.
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Affiliation(s)
- Maryam Sanaee
- Department
of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - K. Göran Ronquist
- Department
of Clinical Sciences, Swedish University
of Agricultural Sciences, Uppsala 75007, Sweden
| | - Elin Sandberg
- Department
of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Jane M. Morrell
- Department
of Clinical Sciences, Swedish University
of Agricultural Sciences, Uppsala 75007, Sweden
| | - Jerker Widengren
- Department
of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm 10691, Sweden
| | - Katia Gallo
- Department
of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm 10691, Sweden
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3
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Sarkar B, Ishii K, Tahara T. Pulsed-Interleaved-Excitation Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. J Phys Chem B 2024; 128:4685-4695. [PMID: 38692581 PMCID: PMC11104349 DOI: 10.1021/acs.jpcb.4c01224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024]
Abstract
We report on pulsed-interleaved-excitation two-dimensional fluorescence lifetime correlation spectroscopy (PIE 2D FLCS) to study biomolecular structural dynamics with high sensitivity and high time resolution using Förster resonance energy transfer (FRET). PIE 2D FLCS is an extension of 2D FLCS, which is a unique single-molecule fluorescence method that uses fluorescence lifetime information to distinguish different fluorescence species in equilibrium and resolves their interconversion dynamics with a submicrosecond time resolution. Because 2D FLCS has used only a single-color excitation so far, it was difficult to distinguish a very low-FRET (or zero-FRET) species from only donor-labeled species. We overcome this difficulty by implementing the PIE scheme (i.e., alternate excitation of the donor and acceptor dyes using two temporally interleaved excitations with different colors) to 2D FLCS, realizing two-color excitation and two-color fluorescence detection in 2D FLCS. After proof-of-principle PIE 2D FLCS analysis on the photon data synthesized with Monte Carlo simulation, we apply PIE 2D FLCS to a DNA-hairpin sample and show that this method readily distinguishes four fluorescent species, i.e., high-FRET, low-FRET, and two single-dye-labeled species. In addition, we show that PIE 2D FLCS can also quantitatively evaluate the contributions of the donor-acceptor spectral crosstalk, which often appears as artifacts in FRET studies and degrades the information obtained.
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Affiliation(s)
- Bidyut Sarkar
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Kunihiko Ishii
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast
Spectroscopy Research Team, RIKEN Center
for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
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4
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Liu J, Yu W, Dong C, Huang X, Ren J. Objective scanning-based fluorescence cross-correlation spectroscopy (Scan-FCCS) for studying the fusion dynamics of protein phase separation. Analyst 2024; 149:2719-2727. [PMID: 38525957 DOI: 10.1039/d4an00264d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Protein phase separation plays a very important role in many biological processes and is closely related to the occurrence and development of some serious diseases. So far, the fluorescence imaging method and fluorescence correlation spectroscopy (FCS) have been frequently used to study the phase separation behavior of proteins. Due to the wide size distribution of protein condensates in phase separation from nano-scale to micro-scale in solution and living cells, it is difficult for the fluorescence imaging method and conventional FCS to fully reflect the real state of protein phase separation in the solution due to the low spatio-temporal resolution of the conventional fluorescence imaging method and the limited detection area of FCS. Here, we proposed a novel method for studying the protein phase separation process by objective scanning-based fluorescence cross-correlation spectroscopy (Scan-FCCS). In this study, CRDBP proteins were used as a model and respectively fused with fluorescent proteins (EGFP and mCherry). We first compared conventional FCS and Scan-FCS methods for characterizing the CRDBP protein phase separation behaviors and found that the reproducibility of Scan-FCS is significantly improved by the scanning mode. We studied the self-fusion process of mCherry-CRDBP and EGFP-CRDBP and observed that the phase change concentration of CRDBP was 25 nM and the fusion of mCherry-CRDBP and EGFP-CRDBP at 500 nM was completed within 70 min. We studied the effects of salt concentration and molecular crowding agents on the phase separation of CRDBP and found that salt can prevent the self-fusion of CRDBP and molecular crowding agents can improve the self-fusion of CRDBP. Furthermore, we found the recruitment behavior of CRDBP to β-catenin proteins and studied their recruitment dynamics. Compared to conventional FCS, Scan-FCCS can significantly improve the reproducibility of measurements due to the dramatic increase of detection zone, and more importantly, this method can provide information about self-fusion and recruitment dynamics in protein phase separation.
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Affiliation(s)
- Jian Liu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Wenxin Yu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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5
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Clark BS, Silvernail I, Gordon K, Castaneda JF, Morgan AN, Rolband LA, LeBlanc SJ. A practical guide to time-resolved fluorescence microscopy and spectroscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577300. [PMID: 38586000 PMCID: PMC10996486 DOI: 10.1101/2024.01.25.577300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Time-correlated single photon counting (TCSPC) coupled with confocal microscopy is a versatile biophysical tool that enables real-time monitoring of biomolecular dynamics across many timescales. With TCSPC, Fluorescence correlation spectroscopy (FCS) and pulsed interleaved excitation-Förster resonance energy transfer (PIE-FRET) are collected simultaneously on diffusing molecules to extract diffusion characteristics and proximity information. This article is a guide to calibrating FCS and PIE-FRET measurements with several biological samples including liposomes, streptavidin-coated quantum dots, proteins, and nucleic acids for reliable determination of diffusion coefficients and FRET efficiency. The FRET efficiency results are also compared to surface-attached single molecules using fluorescence lifetime imaging microscopy (FLIM-FRET). Combining the methods is a powerful approach to revealing mechanistic details of biological processes and pathways.
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6
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Alfonso C, Sobrinos-Sanguino M, Luque-Ortega JR, Zorrilla S, Monterroso B, Nuero OM, Rivas G. Studying Macromolecular Interactions of Cellular Machines by the Combined Use of Analytical Ultracentrifugation, Light Scattering, and Fluorescence Spectroscopy Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:89-107. [PMID: 38507202 DOI: 10.1007/978-3-031-52193-5_7] [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: 03/22/2024]
Abstract
Cellular machines formed by the interaction and assembly of macromolecules are essential in many processes of the living cell. These assemblies involve homo- and hetero-associations, including protein-protein, protein-DNA, protein-RNA, and protein-polysaccharide associations, most of which are reversible. This chapter describes the use of analytical ultracentrifugation, light scattering, and fluorescence-based methods, well-established biophysical techniques, to characterize interactions leading to the formation of macromolecular complexes and their modulation in response to specific or unspecific factors. We also illustrate, with several examples taken from studies on bacterial processes, the advantages of the combined use of subsets of these techniques as orthogonal analytical methods to analyze protein oligomerization and polymerization, interactions with ligands, hetero-associations involving membrane proteins, and protein-nucleic acid complexes.
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Affiliation(s)
- Carlos Alfonso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Marta Sobrinos-Sanguino
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Silvia Zorrilla
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Begoña Monterroso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar M Nuero
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Germán Rivas
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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7
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Zhang C, Brunt L, Ono Y, Rogers S, Scholpp S. Cytoneme-mediated transport of active Wnt5b-Ror2 complexes in zebrafish. Nature 2024; 625:126-133. [PMID: 38123680 PMCID: PMC10764289 DOI: 10.1038/s41586-023-06850-7] [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: 05/13/2022] [Accepted: 11/08/2023] [Indexed: 12/23/2023]
Abstract
Chemical signalling is the primary means by which cells communicate in the embryo. The underlying principle refers to a group of ligand-producing cells and a group of cells that respond to this signal because they express the appropriate receptors1,2. In the zebrafish embryo, Wnt5b binds to the receptor Ror2 to trigger the Wnt-planar cell polarity (PCP) signalling pathway to regulate tissue polarity and cell migration3,4. However, it remains unclear how this lipophilic ligand is transported from the source cells through the aqueous extracellular space to the target tissue. In this study, we provide evidence that Wnt5b, together with Ror2, is loaded on long protrusions called cytonemes. Our data further suggest that the active Wnt5b-Ror2 complexes form in the producing cell and are handed over from these cytonemes to the receiving cell. Then, the receiving cell has the capacity to initiate Wnt-PCP signalling, irrespective of its functional Ror2 receptor status. On the tissue level, we further show that cytoneme-dependent spreading of active Wnt5b-Ror2 affects convergence and extension in the zebrafish gastrula. We suggest that cytoneme-mediated transfer of ligand-receptor complexes is a vital mechanism for paracrine signalling. This may prompt a reevaluation of the conventional concept of characterizing responsive and non-responsive tissues solely on the basis of the expression of receptors.
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Affiliation(s)
- Chengting Zhang
- Living Systems Institute, School of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Lucy Brunt
- Living Systems Institute, School of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Yosuke Ono
- Living Systems Institute, School of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Sally Rogers
- Living Systems Institute, School of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Steffen Scholpp
- Living Systems Institute, School of Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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8
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Liu J, Yu S, Yu W, Dong C, Huang X, Ren J. CRDBP Protein Phase Separation and Its Recruitment to β-Catenin Protein in a Single Living Cell. J Phys Chem B 2023; 127:10498-10507. [PMID: 38051203 DOI: 10.1021/acs.jpcb.3c06346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The Coding Region Determinant-Binding Protein (CRDBP) is a carcinoembryonic protein, and it is overexpressed in various cancer cells in the form of granules. We speculated the formation of CRDBP granules possibly through liquid-liquid phase separation (LLPS) processes due to the existence of intrinsically disordered regions (IDRs) in CRDBP. So far, we did not know whether or how phase separation processes of CRDBP occur in single living cells due to the lack of in vivo methods for studying intracellular protein phase separation. Therefore, to develop an in situ method for studying protein phase separation in living cells is a very urgent task. In this work, we proposed an efficient method for studying phase separation behavior of CRDBP in a single living cell by combining in situ fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) with a fluorescence protein fusion technique. We first predicted and confirmed that CRDBP has phase separation in solution by conventional fluorescence imaging and FCS methods. And then, we in situ studied the phase separation behaviors of CRDBP in living cells and observed three states of CRDBP phase separation such as monomer state, cluster state, and granule state. We studied the effects of CRDBP truncated forms and its inhibitor on the CRDBP phase separation. Furthermore, we discovered the recruitment of CRDBP to β-catenin protein in living cells and investigated the effects of CRDBP structures and inhibitor on CRDBP recruitment behavior. This finding may help us to further understand the mechanism of CRDBP protein for regulating Wnt signaling pathway. Additionally, our results documented that FCS/FCCS is an efficient and alternative method for studying protein phase separation in situ in living cells.
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Affiliation(s)
- Jian Liu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Shengrong Yu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Wenxin Yu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
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9
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Perego E, Zappone S, Castagnetti F, Mariani D, Vitiello E, Rupert J, Zacco E, Tartaglia GG, Bozzoni I, Slenders E, Vicidomini G. Single-photon microscopy to study biomolecular condensates. Nat Commun 2023; 14:8224. [PMID: 38086853 PMCID: PMC10716487 DOI: 10.1038/s41467-023-43969-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Biomolecular condensates serve as membrane-less compartments within cells, concentrating proteins and nucleic acids to facilitate precise spatial and temporal orchestration of various biological processes. The diversity of these processes and the substantial variability in condensate characteristics present a formidable challenge for quantifying their molecular dynamics, surpassing the capabilities of conventional microscopy. Here, we show that our single-photon microscope provides a comprehensive live-cell spectroscopy and imaging framework for investigating biomolecular condensation. Leveraging a single-photon detector array, single-photon microscopy enhances the potential of quantitative confocal microscopy by providing access to fluorescence signals at the single-photon level. Our platform incorporates photon spatiotemporal tagging, which allowed us to perform time-lapse super-resolved imaging for molecular sub-diffraction environment organization with simultaneous monitoring of molecular mobility, interactions, and nano-environment properties through fluorescence lifetime fluctuation spectroscopy. This integrated correlative study reveals the dynamics and interactions of RNA-binding proteins involved in forming stress granules, a specific type of biomolecular condensates, across a wide range of spatial and temporal scales. Our versatile framework opens up avenues for exploring a broad spectrum of biomolecular processes beyond the formation of membrane-less organelles.
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Affiliation(s)
- Eleonora Perego
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Sabrina Zappone
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi, University of Genoa, Genoa, Italy
| | - Francesco Castagnetti
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Davide Mariani
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Erika Vitiello
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Jakob Rupert
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Elsa Zacco
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Gian Gaetano Tartaglia
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy.
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10
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Eisenreichova A, Humpolickova J, Różycki B, Boura E, Koukalova A. Effects of biophysical membrane properties on recognition of phosphatidylserine, or phosphatidylinositol 4-phosphate by lipid biosensors LactC2, or P4M. Biochimie 2023; 215:42-49. [PMID: 37683994 DOI: 10.1016/j.biochi.2023.09.003] [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] [Received: 04/28/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Lipid biosensors are molecular tools used both in vivo and in vitro applications, capable of selectively detecting specific types of lipids in biological membranes. However, despite their extensive use, there is a lack of systematic characterization of their binding properties in various membrane conditions. The purpose of this study was to investigate the impact of membrane properties, such as fluidity and membrane charge, on the sensitivity of two lipid biosensors, LactC2 and P4M, to their target lipids, phosphatidylserine (PS) or phosphatidylinositol 4-phosphate (PI4P), respectively. Dual-color fluorescence cross-correlation spectroscopy, employed in this study, provided a useful technique to investigate interactions of these recombinant fluorescent biosensors with liposomes of varying compositions. The results of the study demonstrate that the binding of the LactC2 biosensor to low levels of PS in the membrane is highly supported by the presence of anionic lipids or membrane fluidity. However, at high PS levels, the presence of anionic lipids does not further enhance binding of LactC2. In contrast, neither membrane charge, nor membrane fluidity significantly affect the binding affinity of P4M to PI4P. These findings provide valuable insights into the role of membrane properties on the binding properties of lipid biosensors.
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Affiliation(s)
- Andrea Eisenreichova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Jana Humpolickova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Alena Koukalova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.
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11
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Hui E. Cis Interactions of Membrane Receptors and Ligands. Annu Rev Cell Dev Biol 2023; 39:391-408. [PMID: 37339682 DOI: 10.1146/annurev-cellbio-120420-103941] [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: 06/22/2023]
Abstract
Cell-cell communication is critical for the development and function of multicellular organisms. A crucial means by which cells communicate with one another is physical interactions between receptors on one cell and their ligands on a neighboring cell. Trans ligand:receptor interactions activate the receptor, ultimately leading to changes in the fate of the receptor-expressing cells. Such trans signaling is known to be critical for the functions of cells in the nervous and immune systems, among others. Historically, trans interactions are the primary conceptual framework for understanding cell-cell communication. However, cells often coexpress many receptors and ligands, and a subset of these has been reported to interact in cis and profoundly impact cell functions. Cis interactions likely constitute a fundamental, understudied regulatory mechanism in cell biology. Here, I discuss how cis interactions between membrane receptors and ligands regulate immune cell functions, and I also highlight outstanding questions in the field.
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Affiliation(s)
- Enfu Hui
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA;
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12
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Ohga N, Ito S, Kolchinsky A. Thermodynamic Bound on the Asymmetry of Cross-Correlations. PHYSICAL REVIEW LETTERS 2023; 131:077101. [PMID: 37656850 DOI: 10.1103/physrevlett.131.077101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/08/2023] [Indexed: 09/03/2023]
Abstract
The principle of microscopic reversibility says that, in equilibrium, two-time cross-correlations are symmetric under the exchange of observables. Thus, the asymmetry of cross-correlations is a fundamental, measurable, and often-used statistical signature of deviation from equilibrium. Here we find a simple and universal inequality that bounds the magnitude of asymmetry by the cycle affinity, i.e., the strength of thermodynamic driving. Our result applies to a large class of systems and all state observables, and it suggests a fundamental thermodynamic cost for various nonequilibrium functions quantified by the asymmetry. It also provides a powerful tool to infer affinity from measured cross-correlations, in a different and complementary way to the thermodynamic uncertainty relations. As an application, we prove a thermodynamic bound on the coherence of noisy oscillations, which was previously conjectured by Barato and Seifert [Phys. Rev. E 95, 062409 (2017)PRESCM2470-004510.1103/PhysRevE.95.062409]. We also derive a thermodynamic bound on directed information flow in a biochemical signal transduction model.
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Affiliation(s)
- Naruo Ohga
- Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sosuke Ito
- Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Universal Biology Institute, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Artemy Kolchinsky
- Universal Biology Institute, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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13
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Gandhi SA, Sanders MA, Granneman JG, Kelly CV. Four-color fluorescence cross-correlation spectroscopy with one laser and one camera. BIOMEDICAL OPTICS EXPRESS 2023; 14:3812-3827. [PMID: 37497523 PMCID: PMC10368031 DOI: 10.1364/boe.486937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 07/28/2023]
Abstract
The diffusion and reorganization of phospholipids and membrane-associated proteins are fundamental for cellular function. Fluorescence cross-correlation spectroscopy (FCCS) measures diffusion and molecular interactions at nanomolar concentration in biological systems. We have developed an economical method to simultaneously monitor diffusion and complexation with the use of super-continuum laser and spectral deconvolution from a single detector. Customizable excitation wavelengths were chosen from the wide-band source and spectral fitting of the emitted light revealed the interactions for up to four chromatically overlapping fluorophores simultaneously. This method was applied to perform four-color FCCS that we demonstrated with polystyrene nanoparticles, lipid vesicles, and membrane-bound molecules. Up to four individually customizable excitation channels were selected from the broad-spectrum fiber laser to excite the diffusers within a diffraction-limited spot. The fluorescence emission passed through a cleanup filter and a dispersive prism prior to being collected by a sCMOS or EMCCD camera with up to 1.8 kHz frame rates. The emission intensity versus time of each fluorophore was extracted through a linear least-square fitting of each camera frame and temporally correlated via custom software. Auto- and cross-correlation functions enabled the measurement of the diffusion rates and binding partners. We have measured the induced aggregation of nanobeads and lipid vesicles in solution upon increasing the buffer salinity. Because of the adaptability of investigating four fluorophores simultaneously with a cost-effective method, this technique will have wide application for examining macromolecular complex formation in model and living systems.
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Affiliation(s)
- Sonali A. Gandhi
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
| | - Matthew A. Sanders
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 40201, USA
| | - James G. Granneman
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 40201, USA
- Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Christopher V. Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
- Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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14
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Ji J, Wang W, Chen C. Single-molecule techniques to visualize and to characterize liquid-liquid phase separation and phase transition. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1023-1033. [PMID: 36876423 PMCID: PMC10415186 DOI: 10.3724/abbs.2023028] [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] [Received: 11/24/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023] Open
Abstract
Biomolecules forming membraneless structures via liquid-liquid phase separation (LLPS) is a common event in living cells. Some liquid-like condensates can convert into solid-like aggregations, and such a phase transition process is related to some neurodegenerative diseases. Liquid-like condensates and solid-like aggregations usually exhibit distinctive fluidity and are commonly distinguished via their morphology and dynamic properties identified through ensemble methods. Emerging single-molecule techniques are a group of highly sensitive techniques, which can offer further mechanistic insights into LLPS and phase transition at the molecular level. Here, we summarize the working principles of several commonly used single-molecule techniques and demonstrate their unique power in manipulating LLPS, examining mechanical properties at the nanoscale, and monitoring dynamic and thermodynamic properties at the molecular level. Thus, single-molecule techniques are unique tools to characterize LLPS and liquid-to-solid phase transition under close-to-physiological conditions.
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Affiliation(s)
- Jinyao Ji
- School of Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructureTsinghua UniversityBeijing100084China
| | - Wenjuan Wang
- School of Life SciencesTechnology Center for Protein SciencesTsinghua UniversityBeijing100084China
| | - Chunlai Chen
- School of Life SciencesBeijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center of Biological StructureTsinghua UniversityBeijing100084China
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15
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Caranfil A, Le Cunff Y, Kervrann C. BayesTICS: Local temporal image correlation spectroscopy and Bayesian simulation technique for sparse estimation of diffusion in fluorescence imaging. BIOLOGICAL IMAGING 2023; 3:e5. [PMID: 38487689 PMCID: PMC10936362 DOI: 10.1017/s2633903x23000041] [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: 05/19/2022] [Revised: 10/29/2022] [Accepted: 01/28/2023] [Indexed: 03/17/2024]
Abstract
The dynamics and fusion of vesicles during the last steps of exocytosis are not well established yet in cell biology. An open issue is the characterization of the diffusion process at the plasma membrane. Total internal reflection fluorescence microscopy (TIRFM) has been successfully used to analyze the coordination of proteins involved in this mechanism. It enables to capture dynamics of proteins with high frame rate and reasonable signal-to-noise values. Nevertheless, methodological approaches that can analyze and estimate diffusion in local small areas at the scale of a single diffusing spot within cells, are still lacking. To address this issue, we propose a novel correlation-based method for local diffusion estimation. As a starting point, we consider Fick's second law of diffusion that relates the diffusive flux to the gradient of the concentration. Then, we derive an explicit parametric model which is further fitted to time-correlation signals computed from regions of interest (ROI) containing individual spots. Our modeling and Bayesian estimation framework are well appropriate to represent isolated diffusion events and are robust to noise, ROI sizes, and localization of spots in ROIs. The performance of BayesTICS is shown on both synthetic and real TIRFM images depicting Transferrin Receptor proteins.
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Affiliation(s)
- Anca Caranfil
- SERPICO Project-Team, INRIA Rennes, UMR144 CNRS Institut Curie, PSL Research, Sorbonne Université, Campus universitaire de Beaulieu, Rennes, France
- CeDRE Team, GDR UMR6290-CNRS, Faculty of Medicine, University of Rennes 1, Rennes, France
| | - Yann Le Cunff
- CeDRE Team, GDR UMR6290-CNRS, Faculty of Medicine, University of Rennes 1, Rennes, France
- Dyliss Team, Univ Rennes, CNRS, Inria, IRISA, UMR 6074, Campus de Beaulieu, Rennes, France
| | - Charles Kervrann
- SERPICO Project-Team, INRIA Rennes, UMR144 CNRS Institut Curie, PSL Research, Sorbonne Université, Campus universitaire de Beaulieu, Rennes, France
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16
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Gandhi SA, Sanders MA, Granneman JG, Kelly CV. Four-color fluorescence cross-correlation spectroscopy with one laser and one camera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526256. [PMID: 36778294 PMCID: PMC9915509 DOI: 10.1101/2023.01.30.526256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The diffusion and reorganization of phospholipids and membrane-associated proteins are fundamental for cellular function. Fluorescence cross-correlation spectroscopy (FCCS) measures the diffusion and molecular interactions at nanomolar concentration in biological systems. We have developed a novel, economical method to simultaneously monitor diffusion and oligomerization with the use of super-continuum laser and spectral deconvolution from a single detector. Customizable excitation wavelengths were chosen from the wide-band source and spectral fitting of the emitted light revealed the interactions for up to four spectrally overlapping fluorophores simultaneously. This method was applied to perform four-color FCCS, as demonstrated with polystyrene nanoparticles, lipid vesicles, and membrane-bound molecules. Up to four individually customizable excitation channels were selected from the broad-spectrum fiber laser to excite the diffusers within a diffraction-limited spot. The fluorescence emission passed through a cleanup filter and a dispersive prism prior to being collected by a sCMOS or EMCCD camera with up to 10 kHz frame rates. The emission intensity versus time of each fluorophore was extracted through a linear least-square fitting of each camera frame and temporally correlated via custom software. Auto- and cross-correlation functions enabled the measurement of the diffusion rates and binding partners. We have measured the induced aggregation of nanobeads and lipid vesicles in solution upon increasing the buffer salinity. Because of the adaptability of investigating four fluorophores simultaneously with a cost-effective method, this technique will have wide application for examining complex homo- and heterooligomerization in model and living systems.
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Affiliation(s)
- Sonali A. Gandhi
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, USA, 48201
| | - Matthew A. Sanders
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA, 40201
| | - James G. Granneman
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA, 40201,Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI, USA. 48201
| | - Christopher V. Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI, USA, 48201,Center for Integrative Metabolic and Endocrine Research, School of Medicine, Wayne State University, Detroit, MI, USA. 48201,Corresponding author:
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17
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Shrinking gate fluorescence correlation spectroscopy yields equilibrium constants and separates photophysics from structural dynamics. Proc Natl Acad Sci U S A 2023; 120:e2211896120. [PMID: 36652471 PMCID: PMC9942831 DOI: 10.1073/pnas.2211896120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Fluorescence correlation spectroscopy is a versatile tool for studying fast conformational changes of biomolecules especially when combined with Förster resonance energy transfer (FRET). Despite the many methods available for identifying structural dynamics in FRET experiments, the determination of the forward and backward transition rate constants and thereby also the equilibrium constant is difficult when two intensity levels are involved. Here, we combine intensity correlation analysis with fluorescence lifetime information by including only a subset of photons in the autocorrelation analysis based on their arrival time with respect to the excitation pulse (microtime). By fitting the correlation amplitude as a function of microtime gate, the transition rate constants from two fluorescence-intensity level systems and the corresponding equilibrium constants are obtained. This shrinking-gate fluorescence correlation spectroscopy (sg-FCS) approach is demonstrated using simulations and with a DNA origami-based model system in experiments on immobilized and freely diffusing molecules. We further show that sg-FCS can distinguish photophysics from dynamic intensity changes even if a dark quencher, in this case graphene, is involved. Finally, we unravel the mechanism of a FRET-based membrane charge sensor indicating the broad potential of the method. With sg-FCS, we present an algorithm that does not require prior knowledge and is therefore easily implemented when an autocorrelation analysis is carried out on time-correlated single-photon data.
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18
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Han S, da Costa Marques R, Simon J, Kaltbeitzel A, Koynov K, Landfester K, Mailänder V, Lieberwirth I. Endosomal sorting results in a selective separation of the protein corona from nanoparticles. Nat Commun 2023; 14:295. [PMID: 36653346 PMCID: PMC9847456 DOI: 10.1038/s41467-023-35902-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
The formation of the protein corona is a well-known effect when nanoparticles (NP) are exposed to biological environments. The protein corona is the most important factor, which determines the rate and route of endocytosis, and decisively impacts cellular processes and even the release of the active pharmaceutical ingredient from the nanoparticles. While many studies concentrate on the effect of the protein corona formation extracellularly or the uptake consequences, little is known about the fate of the protein corona inside of cells. Here, we reconstruct for the first time the separation of the protein corona from the NPs by the cell and their further fate. Ultimately, the NPs and protein corona are separated from each other and end up in morphologically different cellular compartments. The cell directs the NPs towards recycling endosomes, whereas the protein corona gathers in multivesicular bodies. From this, we conclude that the NPs are prepared for subsequent exocytosis, while the protein corona remains in the cell and is finally metabolized there.
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Affiliation(s)
- Shen Han
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Richard da Costa Marques
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Dermatology Clinic, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Johanna Simon
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Dermatology Clinic, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Anke Kaltbeitzel
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Dermatology Clinic, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Ingo Lieberwirth
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
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19
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Löffler T, Krüger A, Zirak P, Winterhalder MJ, Müller AL, Fischbach A, Mangerich A, Zumbusch A. Influence of chain length and branching on poly(ADP-ribose)-protein interactions. Nucleic Acids Res 2023; 51:536-552. [PMID: 36625274 PMCID: PMC9881148 DOI: 10.1093/nar/gkac1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/16/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Hundreds of proteins interact with poly(ADP-ribose) (PAR) via multiple PAR interaction motifs, thereby regulating their physico-chemical properties, sub-cellular localizations, enzymatic activities, or protein stability. Here, we present a targeted approach based on fluorescence correlation spectroscopy (FCS) to characterize potential structure-specific interactions of PAR molecules of defined chain length and branching with three prime PAR-binding proteins, the tumor suppressor protein p53, histone H1, and the histone chaperone APLF. Our study reveals complex and structure-specific PAR-protein interactions. Quantitative Kd values were determined and binding affinities for all three proteins were shown to be in the nanomolar range. We report PAR chain length dependent binding of p53 and H1, yet chain length independent binding of APLF. For all three PAR binders, we found a preference for linear over hyperbranched PAR. Importantly, protein- and PAR-structure-specific binding modes were revealed. Thus, while the H1-PAR interaction occurred largely on a bi-molecular 1:1 basis, p53-and potentially also APLF-can form complex multivalent PAR-protein structures. In conclusion, our study gives detailed and quantitative insight into PAR-protein interactions in a solution-based setting at near physiological buffer conditions. The results support the notion of protein and PAR-structure-specific binding modes that have evolved to fit the purpose of the respective biochemical functions and biological contexts.
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Affiliation(s)
| | | | - Peyman Zirak
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | | | - Anna-Lena Müller
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | - Arthur Fischbach
- Department of Biology, Universität Konstanz, Konstanz D-78457, Germany
| | - Aswin Mangerich
- To whom correspondence should be addressed. Tel: +49 33200 88 5301;
| | - Andreas Zumbusch
- Correspondence may also be addressed to Andreas Zumbusch. Tel: +49 7531 882027;
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20
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Díaz M, Malacrida L. Advanced Fluorescence Microscopy Methods to Study Dynamics of Fluorescent Proteins In Vivo. Methods Mol Biol 2023; 2564:53-74. [PMID: 36107337 DOI: 10.1007/978-1-0716-2667-2_3] [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: 06/15/2023]
Abstract
Fluorescent proteins are standard tools for addressing biological questions in a cell biology laboratory. The genetic tagging of protein of interest with fluorescent proteins opens the opportunity to follow them in vivo and to understand their interactions and dynamics. In addition, the latest advances in optical microscopy image acquisition and processing allow us to study many cellular processes in vivo. Techniques such as fluorescence lifetime microscopy and hyperspectral imaging provide valuable tools for understanding fluorescent protein interactions and their photophysics. Finally, fluorescence fluctuation analysis opens the possibility to address questions of molecular diffusion, protein-protein interactions, and oligomerization, among others, yielding quantitative information on the subject of study. This chapter will cover some of the more important advances in cutting-edge technologies and methods that, combined with fluorescent proteins, open new frontiers for biological studies.
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Affiliation(s)
- Marcela Díaz
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo & Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo & Universidad de la República, Montevideo, Uruguay.
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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21
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Abstract
The sensitivity of the αβ T cell receptor (TCR) is enhanced by the coreceptors CD4 and CD8αβ, which are expressed primarily by cells of the helper and cytotoxic T cell lineages, respectively. The coreceptors bind to major histocompatibility complex (MHC) molecules and associate intracellularly with the Src-family kinase Lck, which catalyzes TCR phosphorylation during receptor triggering. Although coreceptor/kinase occupancy was initially believed to be high, a recent study suggested that most coreceptors exist in an Lck-free state, and that this low occupancy helps to effect TCR antigen discrimination. Here, using the same method, we found instead that the CD4/Lck interaction was stoichiometric (~100%) and that the CD8αβ/Lck interaction was substantial (~60%). We confirmed our findings in live cells using fluorescence cross-correlation spectroscopy (FCCS) to measure coreceptor/Lck codiffusion in situ. After introducing structurally guided mutations into the intracellular domain of CD4, we used FCCS to also show that stoichiometric coupling to Lck required an amphipathic α-helix present in CD4 but not CD8α. In double-positive cells expressing equal numbers of both coreceptors, but limiting amounts of kinase, CD4 outcompeted CD8αβ for Lck. In T cells, TCR signaling induced CD4/Lck oligomerization but did not affect the high levels of CD4/Lck occupancy. These findings help settle the question of kinase occupancy and suggest that the binding advantages that CD4 has over CD8 could be important when Lck levels are limiting.
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22
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Kishimoto T, Masui K, Minoshima W, Hosokawa C. Recent advances in optical manipulation of cells and molecules for biological science. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Sefer A, Kallis E, Eilert T, Röcker C, Kolesnikova O, Neuhaus D, Eustermann S, Michaelis J. Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level. Nat Commun 2022; 13:6569. [PMID: 36323657 PMCID: PMC9630430 DOI: 10.1038/s41467-022-34148-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1's multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1's N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.
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Affiliation(s)
- Anna Sefer
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Eleni Kallis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Tobias Eilert
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Boehringer Ingelheim, CoC CMC Statistics & Data Science, Birkendorfer Str. 65, 88400, Biberach, Germany
| | - Carlheinz Röcker
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Olga Kolesnikova
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - Jens Michaelis
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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24
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Hetero-pentamerization determines mobility and conductance of Glycine receptor α3 splice variants. Cell Mol Life Sci 2022; 79:540. [PMID: 36197517 PMCID: PMC9534812 DOI: 10.1007/s00018-022-04506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/05/2022]
Abstract
Glycine receptors (GlyRs) are ligand-gated pentameric chloride channels in the central nervous system. GlyR-α3 is a possible target for chronic pain treatment and temporal lobe epilepsy. Alternative splicing into K or L variants determines the subcellular fate and function of GlyR-α3, yet it remains to be shown whether its different splice variants can functionally co-assemble, and what the properties of such heteropentamers would be. Here, we subjected GlyR-α3 to a combined fluorescence microscopy and electrophysiology analysis. We employ masked Pearson’s and dual-color spatiotemporal correlation analysis to prove that GlyR-α3 splice variants heteropentamerize, adopting the mobility of the K variant. Fluorescence-based single-subunit counting experiments revealed a variable and concentration ratio dependent hetero-stoichiometry. Via cell-attached single-channel electrophysiology we show that heteropentamers exhibit currents in between those of K and L variants. Our data are compatible with a model where α3 heteropentamerization fine-tunes mobility and activity of GlyR-α3 channels, which is important to understand and tackle α3 related diseases.
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25
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Opanasyuk O, Barth A, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CA. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. II. Quantitative analysis of multi-state kinetic networks. J Chem Phys 2022; 157:031501. [DOI: 10.1063/5.0095754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) experiments are ideally suited to resolve the structural dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly when these dynamics occur on the sub-millisecond timescale. Many methods for quantitative analysis are challenged if more than two states are involved, and the appropriate choice of the number of states in the kinetic network is difficult. An additional complication arises if dynamically active molecules coexist with pseudo-static molecules in similar conformational states with undistinguishable FRET efficiencies. To address these problems, we developed a quantitative integrative analysis framework that combines the information from FRET-lines that relate average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms, fluorescence decays obtained by time-correlated single photon counting, photon distribution analysis of the intensities and fluorescence correlation spectroscopy. Individually, these methodologies provide ambiguous results for the characterization of dynamics in complex kinetic networks. However, the global analysis approach enables accurate determination of the number of states, their kinetic connectivity, the transition rate constants, and species fractions. To challenge the potential of smFRET experiments studying multi-state kinetic networks, we apply our integrative framework using a set of synthetic data for three-state systems with different kinetic connectivity and exchange rates. Our methodology paves the way towards an integrated analysis of multiparameter smFRET experiments that spans all dimensions of the experimental data. Finally, we propose a workflow for the analysis and show examples that demonstrate the usefulness of this toolkit for dynamic structural biology.
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Affiliation(s)
| | | | | | - Suren Felekyan
- PC-II, Heinrich Heine University Düsseldorf Department of Chemistry, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
| | | | - Claus A.M. Seidel
- Institut fuer Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
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26
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Galiani S, Reglinski K, Carravilla P, Barbotin A, Urbančič I, Ott J, Sehr J, Sezgin E, Schneider F, Waithe D, Hublitz P, Schliebs W, Erdmann R, Eggeling C. Diffusion and interaction dynamics of the cytosolic peroxisomal import receptor PEX5. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 36299769 PMCID: PMC9586885 DOI: 10.1016/j.bpr.2022.100055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/24/2022] [Indexed: 11/18/2022]
Abstract
Cellular functions rely on proper actions of organelles such as peroxisomes. These organelles rely on the import of proteins from the cytosol. The peroxisomal import receptor PEX5 takes up target proteins in the cytosol and transports them to the peroxisomal matrix. However, its cytosolic molecular interactions have so far not directly been disclosed. Here, we combined advanced optical microscopy and spectroscopy techniques such as fluorescence correlation spectroscopy and stimulated emission depletion microscopy with biochemical tools to present a detailed characterization of the cytosolic diffusion and interaction dynamics of PEX5. Among other features, we highlight a slow diffusion of PEX5, independent of aggregation or target binding, but associated with cytosolic interaction partners via its N-terminal domain. This sheds new light on the functionality of the receptor in the cytosol as well as highlighting the potential of using complementary microscopy tools to decipher molecular interactions in the cytosol by studying their diffusion dynamics.
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Affiliation(s)
- S. Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - K. Reglinski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- University Hospital Jena, Jena, Germany
| | - P. Carravilla
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
| | - A. Barbotin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - I. Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Laboratory of Biophysics, Condensed Matter Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
| | - J. Ott
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - J. Sehr
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - E. Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
| | - F. Schneider
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - D. Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- WIMM Centre for Computational Biology , MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - P. Hublitz
- WIMM Genome Engineering Services, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - W. Schliebs
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - R. Erdmann
- Institute of Biochemistry and Pathobiochemistry, Systems Biochemistry, Ruhr-University Bochum, Bochum, Germany
| | - C. Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Leibniz-Institute of Photonic Technologies e.V., Jena, Germany
- Institute of Applied Optic and Biophysics, Friedrich-Schiller University Jena, Jena, Germany
- Jena Center for Soft Matter (JCSM), Jena, Germany
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27
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Barbiero M, Cirillo L, Veerapathiran S, Coates C, Ruffilli C, Pines J. Cell cycle-dependent binding between Cyclin B1 and Cdk1 revealed by time-resolved fluorescence correlation spectroscopy. Open Biol 2022; 12:220057. [PMID: 35765818 PMCID: PMC9240681 DOI: 10.1098/rsob.220057] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/07/2022] [Indexed: 01/04/2023] Open
Abstract
Measuring the dynamics with which the regulatory complexes assemble and disassemble is a crucial barrier to our understanding of how the cell cycle is controlled that until now has been difficult to address. This considerable gap in our understanding is due to the difficulty of reconciling biochemical assays with single cell-based techniques, but recent advances in microscopy and gene editing techniques now enable the measurement of the kinetics of protein-protein interaction in living cells. Here, we apply fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy to study the dynamics of the cell cycle machinery, beginning with Cyclin B1 and its binding to its partner kinase Cdk1 that together form the major mitotic kinase. Although Cyclin B1 and Cdk1 are known to bind with high affinity, our results reveal that in living cells there is a pool of Cyclin B1 that is not bound to Cdk1. Furthermore, we provide evidence that the affinity of Cyclin B1 for Cdk1 increases during the cell cycle, indicating that the assembly of the complex is a regulated step. Our work lays the groundwork for studying the kinetics of protein complex assembly and disassembly during the cell cycle in living cells.
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Affiliation(s)
- Martina Barbiero
- Cancer Biology, The Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London, London SW3 6JB, UK
| | - Luca Cirillo
- Cancer Biology, The Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London, London SW3 6JB, UK
| | - Sapthaswaran Veerapathiran
- Cancer Biology, The Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London, London SW3 6JB, UK
| | - Catherine Coates
- Cancer Biology, The Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London, London SW3 6JB, UK
| | - Camilla Ruffilli
- Cancer Biology, The Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London, London SW3 6JB, UK
| | - Jonathon Pines
- Cancer Biology, The Institute of Cancer Research Chester Beatty Laboratories, 237 Fulham Road, London, London SW3 6JB, UK
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28
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Laurence MJ, Carpenter TS, Laurence TA, Coleman MA, Shelby M, Liu C. Biophysical Characterization of Membrane Proteins Embedded in Nanodiscs Using Fluorescence Correlation Spectroscopy. MEMBRANES 2022; 12:membranes12040392. [PMID: 35448362 PMCID: PMC9028781 DOI: 10.3390/membranes12040392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023]
Abstract
Proteins embedded in biological membranes perform essential functions in all organisms, serving as receptors, transporters, channels, cell adhesion molecules, and other supporting cellular roles. These membrane proteins comprise ~30% of all human proteins and are the targets of ~60% of FDA-approved drugs, yet their extensive characterization using established biochemical and biophysical methods has continued to be elusive due to challenges associated with the purification of these insoluble proteins. In response, the development of nanodisc techniques, such as nanolipoprotein particles (NLPs) and styrene maleic acid polymers (SMALPs), allowed membrane proteins to be expressed and isolated in solution as part of lipid bilayer rafts with defined, consistent nanometer sizes and compositions, thus enabling solution-based measurements. Fluorescence correlation spectroscopy (FCS) is a relatively simple yet powerful optical microscopy-based technique that yields quantitative biophysical information, such as diffusion kinetics and concentrations, about individual or interacting species in solution. Here, we first summarize current nanodisc techniques and FCS fundamentals. We then provide a focused review of studies that employed FCS in combination with nanodisc technology to investigate a handful of membrane proteins, including bacteriorhodopsin, bacterial division protein ZipA, bacterial membrane insertases SecYEG and YidC, Yersinia pestis type III secretion protein YopB, yeast cell wall stress sensor Wsc1, epidermal growth factor receptor (EGFR), ABC transporters, and several G protein-coupled receptors (GPCRs).
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Affiliation(s)
- Matthew J. Laurence
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Timothy S. Carpenter
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
| | - Ted A. Laurence
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA;
| | - Matthew A. Coleman
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Department of Radiation Oncology, University of California Davis, Sacramento, CA 95616, USA
| | - Megan Shelby
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
| | - Chao Liu
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA; (M.J.L.); (T.S.C.); (M.A.C.)
- Correspondence: (M.S.); (C.L.)
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29
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Sanaee M, Sandberg E, Ronquist KG, Morrell JM, Widengren J, Gallo K. Coincident Fluorescence-Burst Analysis of the Loading Yields of Exosome-Mimetic Nanovesicles with Fluorescently-Labeled Cargo Molecules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106241. [PMID: 35084110 DOI: 10.1002/smll.202106241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/11/2021] [Indexed: 06/14/2023]
Abstract
The possible targeting functionality and low immunogenicity of exosomes and exosome-like nanovesicles make them promising as drug-delivery carriers. To tap into this potential, accurate non-destructive methods to load them and characterize their contents are of utmost importance. However, the small size, polydispersity, and aggregation of nanovesicles in solution make quantitative characterizations of their loading particularly challenging. Here, an ad-hoc methodology is developed based on burst analysis of dual-color confocal fluorescence microscopy experiments, suited for quantitative characterizations of exosome-like nanovesicles and of their fluorescently-labeled loading. It is applied to study exosome-mimetic nanovesicles derived from animal extracellular-vesicles and human red blood cell detergent-resistant membranes, loaded with fluorescently-tagged dUTP cargo molecules. For both classes of nanovesicles, successful loading is proved and by dual-color coincident fluorescence burst analysis, size statistics and loading yields are retrieved and quantified. The procedure affords single-vesicle characterizations well-suited for the investigation of a variety of cargo molecules and biological nanovesicle combinations besides the proof-of-principle demonstrations of this study. The results highlight a powerful characterization tool essential for optimizing the loading process and for advanced engineering of biomimetic nanovesicles for therapeutic drug delivery.
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Affiliation(s)
- Maryam Sanaee
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
| | - Elin Sandberg
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
| | - K Göran Ronquist
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
- Oblique Therapeutics AB, Gothenburg, 41346, Sweden
| | - Jane M Morrell
- Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, 75007, Sweden
| | - Jerker Widengren
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
| | - Katia Gallo
- Department of Applied Physics, School of Engineering Sciences, KTH Royal Institute of Technology, Stockholm, 10691, Sweden
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30
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Schmitt S, Nuhn L, Barz M, Butt HJ, Koynov K. Shining Light on Polymeric Drug Nanocarriers with Fluorescence Correlation Spectroscopy. Macromol Rapid Commun 2022; 43:e2100892. [PMID: 35174569 DOI: 10.1002/marc.202100892] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/04/2022] [Indexed: 11/07/2022]
Abstract
The use of nanoparticles as carriers is an extremely promising way for administration of therapeutic agents, such as drug molecules, proteins and nucleic acids. Such nanocarriers (NCs) can increase the solubility of hydrophobic compounds, protect their cargo from the environment, and if properly functionalized, deliver it to specific target cells and tissues. Polymer-based NCs are especially promising, because they offer high degree of versatility and tunability. However, in order to get a full advantage of this therapeutic approach and develop efficient delivery systems, a careful characterization of the NCs is needed. This Feature Article highlights the fluorescence correlation spectroscopy (FCS) technique as a powerful and versatile tool for NCs characterization at all stages of the drug delivery process. In particular, FCS can monitor and quantify the size of the NCs and the drug loading efficiency after preparation, the NCs stability and possible interactions with, e.g., plasma proteins in the blood stream and the kinetic of drug release in the cytoplasm of the target cells. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sascha Schmitt
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Lutz Nuhn
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Matthias Barz
- Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
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31
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Nieto-Garai JA, Lorizate M, Contreras FX. Shedding light on membrane rafts structure and dynamics in living cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183813. [PMID: 34748743 DOI: 10.1016/j.bbamem.2021.183813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/12/2022]
Abstract
Cellular membranes are fundamental building blocks regulating an extensive repertoire of biological functions. These structures contain lipids and membrane proteins that are known to laterally self-aggregate in the plane of the membrane, forming defined membrane nanoscale domains essential for protein activity. Membrane rafts are described as heterogeneous, dynamic, and short-lived cholesterol- and sphingolipid-enriched membrane nanodomains (10-200 nm) induced by lipid-protein and lipid-lipid interactions. Those membrane nanodomains have been extensively characterized using model membranes and in silico methods. However, despite the development of advanced fluorescence microscopy techniques, undoubted nanoscale visualization by imaging techniques of membrane rafts in the membrane of unperturbed living cells is still uncompleted, increasing the skepticism about their existence. Here, we broadly review recent biochemical and microscopy techniques used to investigate membrane rafts in living cells and we enumerate persistent open questions to answer before unlocking the mystery of membrane rafts in living cells.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain.
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Bilbao, Spain
| | - F-Xabier Contreras
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Bilbao, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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32
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Grothe T, Walla PJ. Building and Using a Two-Photon Fluorescence Cross-Correlation Spectroscopy Setup Including Fluorescence Lifetime Analysis. Methods Mol Biol 2022; 2417:147-166. [PMID: 35099798 DOI: 10.1007/978-1-0716-1916-2_12] [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: 06/14/2023]
Abstract
Fluorescence Cross-Correlation Spectroscopy (FCCS) is a well-established and useful tool in physics and chemistry. Furthermore, due to its hybrid character of being a bulk assay at a single molecular level, it found many applications in biophysics and molecular biochemistry. Examples may be investigating kinetics and dynamics of chemical and biochemical reactions such as protein-ligand-, protein-protein-binding, fast conformational changes, and intracellular transportation. Also, it was utilized to characterize larger structures such as lipid vesicles and multi-protein complexes. A two-photon excitation source makes FCCS relatively easy-to-use and easy-to-maintain. Combining this technique with fluorescence lifetime analysis results in a versatile biophysical tool that can be used to solve many biological problems, as even small changes in the local environment, like pH or salt concentration, can be monitored if appropriate fluorophores are used. An example of its use for membrane docking and fusion assays is described in Chap. 13 . In this chapter, we want to give the reader a simple, detailed step-by-step guide of how to set up such a tool.
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Affiliation(s)
- Tobias Grothe
- Laboratory of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Biophysical Chemistry, Institute for Physical and Theoretical Chemistry, Braunschweig, Germany
| | - Peter J Walla
- Laboratory of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
- Department of Biophysical Chemistry, Institute for Physical and Theoretical Chemistry, Braunschweig, Germany.
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33
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Blakemore RJ, Burnett C, Swanson C, Kharytonchyk S, Telesnitsky A, Munro JB. Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR. Biophys J 2021; 120:4874-4890. [PMID: 34529947 PMCID: PMC8595565 DOI: 10.1016/j.bpj.2021.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
During HIV-1 assembly, the viral Gag polyprotein specifically selects the dimeric RNA genome for packaging into new virions. The 5′ untranslated region (5′UTR) of the dimeric genome may adopt a conformation that is optimal for recognition by Gag. Further conformational rearrangement of the 5′UTR, promoted by the nucleocapsid (NC) domain of Gag, is predicted during virus maturation. Two 5′UTR dimer conformations, the kissing dimer (KD) and the extended dimer (ED), have been identified in vitro, which differ in the extent of intermolecular basepairing. Whether 5′UTRs from different HIV-1 strains with distinct sequences have access to the same dimer conformations has not been determined. Here, we applied fluorescence cross-correlation spectroscopy and single-molecule Förster resonance energy transfer imaging to demonstrate that 5′UTRs from two different HIV-1 subtypes form (KDs) with divergent stabilities. We further show that both 5′UTRs convert to a stable dimer in the presence of the viral NC protein, adopting a conformation consistent with extensive intermolecular contacts. These results support a unified model in which the genomes of diverse HIV-1 strains adopt an ED conformation.
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Affiliation(s)
- Robert J Blakemore
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Graduate Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Canessa Swanson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore Country, Baltimore, Maryland
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.
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34
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Sparrenberg LT, Greiner B, Mathis HP. The Mean Single Molecule Rate (mSMR) in the Analysis of Fluorescence Fluctuations: Measurements on DNA Mixtures of Defined Composition. J Fluoresc 2021; 31:1883-1894. [PMID: 34529200 PMCID: PMC8547212 DOI: 10.1007/s10895-021-02803-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/11/2021] [Indexed: 12/03/2022]
Abstract
We present a method for the evaluation of fluorescence fluctuations on the basis of Mandel’s Q parameter, using sampling time-dependent factorial cumulants. By relating the Q parameter to the sampling time, we obtain the mean single molecule rate (mSMR), an easy to interpret expression that provides both brightness and diffusion information. The model is suitable for the widely used confocal setups with single photon excitation and a single detection channel. We present a way to correct the mSMR for afterpulsing, dead time and background noise. To account for photokinetic effects at short sampling times, we expand the model by a simple on/off isomerization term, which is similar to the well-known triplet model. The functionality of the mSMR is shown using Monte Carlo simulations. The correction mechanisms and the experimental applicability of the model are then demonstrated by DNA measurements of defined composition. By systematically analyzing DNA mixtures, we can show that at large sampling times, the mSMR correctly describes the single molecule brightness rates and the diffusive properties of DNA molecules. At short sampling times, the photokinetic effects of isomerization are accurately described by the mSMR model. Since additionally the mSMR can easily be corrected for measurement artefacts such as detector dead time, afterpulsing and background noise, this is a valuable advantage over the standard method of fluorescence correlation spectroscopy.
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Affiliation(s)
- Lorenz T Sparrenberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany. .,Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany.
| | - Benjamin Greiner
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
| | - Harald P Mathis
- Fraunhofer Institute for Applied Information Technology FIT, Schloss Birlinghoven 1, 53757, Sankt Augustin, Germany
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35
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Dunsing V, Petrich A, Chiantia S. Multicolor fluorescence fluctuation spectroscopy in living cells via spectral detection. eLife 2021; 10:e69687. [PMID: 34494547 PMCID: PMC8545396 DOI: 10.7554/elife.69687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/07/2021] [Indexed: 01/20/2023] Open
Abstract
Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about intermolecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion, and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.
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Affiliation(s)
- Valentin Dunsing
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Annett Petrich
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
| | - Salvatore Chiantia
- Universität Potsdam, Institute of Biochemistry and BiologyPotsdamGermany
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36
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Ghosh A, Enderlein J. Advanced fluorescence correlation spectroscopy for studying biomolecular conformation. Curr Opin Struct Biol 2021; 70:123-131. [PMID: 34371261 DOI: 10.1016/j.sbi.2021.06.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 10/20/2022]
Abstract
We present the recent developments and advances in fluorescence correlation spectroscopy (FCS) and their application to the investigation of biomolecular conformations. In particular, we present and discuss three techniques: multichannel nanosecond FCS, photo-induced electron transfer FCS, and fluorescence lifetime correlation spectroscopy. We briefly describe each method and discuss recent applications to diverse biophysical studies of biomolecular conformation.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics, Biophysics, University of Göttingen, Friedrich Hund Platz 1 Göttingen, 37077, Germany
| | - Jörg Enderlein
- Third Institute of Physics, Biophysics, University of Göttingen, Friedrich Hund Platz 1 Göttingen, 37077, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Göttingen, 37077, Germany.
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37
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Yoshida S, Kisley L. Super-resolution fluorescence imaging of extracellular environments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 257:119767. [PMID: 33862370 DOI: 10.1016/j.saa.2021.119767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
The extracellular matrix (ECM) is an important biophysical environment that plays a role in a number of physiological processes. The ECM is highly dynamic, with changes occurring as local, nanoscale, physicochemical variations in physical confinement and chemistry from the perspective of biological molecules. The length and time scale of ECM dynamics are challenging to measure with current spectroscopic techniques. Super-resolution fluorescence microscopy has the potential to probe local, nanoscale, physicochemical variations in the ECM. Here, we review super-resolution imaging and analysis methods and their application to study model nanoparticles and biomolecules within synthetic ECM hydrogels and the brain extracellular space (ECS). We provide a perspective of future directions for the field that can move super-resolution imaging of the ECM towards more biomedically-relevant samples. Overall, super-resolution imaging is a powerful tool that can increase our understanding of extracellular environments at new spatiotemporal scales to reveal ECM processes at the molecular-level.
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Affiliation(s)
- Shawn Yoshida
- Department of Physics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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38
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Jakobowska I, Becker F, Minguzzi S, Hansen K, Henke B, Epalle NH, Beitz E, Hannus S. Fluorescence Cross-Correlation Spectroscopy Yields True Affinity and Binding Kinetics of Plasmodium Lactate Transport Inhibitors. Pharmaceuticals (Basel) 2021; 14:ph14080757. [PMID: 34451854 PMCID: PMC8399565 DOI: 10.3390/ph14080757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 01/13/2023] Open
Abstract
Blocking lactate export in the parasitic protozoan Plasmodium falciparum is a novel strategy to combat malaria. We discovered small drug-like molecules that inhibit the sole plasmodial lactate transporter, PfFNT, and kill parasites in culture. The pentafluoro-3-hydroxy-pent-2-en-1-one BH296 blocks PfFNT with nanomolar efficiency but an in vitro selected PfFNT G107S mutation confers resistance against the drug. We circumvented the mutation by introducing a nitrogen atom as a hydrogen bond acceptor site into the aromatic ring of the inhibitor yielding BH267.meta. The current PfFNT inhibitor efficiency values were derived from yeast-based lactate transport assays, yet direct affinity and binding kinetics data are missing. Here, we expressed PfFNT fused with a green fluorescent protein in human embryonic kidney cells and generated fluorescent derivatives of the inhibitors, BH296 and BH267.meta. Using confocal imaging, we confirmed the location of the proposed binding site at the cytosolic transporter entry site. We then carried out fluorescence cross-correlation spectroscopy measurements to assign true Ki-values, as well as kon and koff rate constants for inhibitor binding to PfFNT wildtype and the G107S mutant. BH296 and BH267.meta gave similar rate constants for binding to PfFNT wildtype. BH296 was inactive on PfFNT G107S, whereas BH267.meta bound the mutant protein albeit with weaker affinity than to PfFNT wildtype. Eventually, using a set of PfFNT inhibitor compounds, we found a robust correlation of the results from the biophysical FCCS binding assay to inhibition data of the functional transport assay.
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Affiliation(s)
- Iga Jakobowska
- Intana Bioscience GmbH, Lochhamer Str. 29a, 82152 Planegg, Germany; (I.J.); (F.B.); (S.M.); (K.H.)
| | - Frank Becker
- Intana Bioscience GmbH, Lochhamer Str. 29a, 82152 Planegg, Germany; (I.J.); (F.B.); (S.M.); (K.H.)
| | - Stefano Minguzzi
- Intana Bioscience GmbH, Lochhamer Str. 29a, 82152 Planegg, Germany; (I.J.); (F.B.); (S.M.); (K.H.)
| | - Kerrin Hansen
- Intana Bioscience GmbH, Lochhamer Str. 29a, 82152 Planegg, Germany; (I.J.); (F.B.); (S.M.); (K.H.)
| | - Björn Henke
- Pharmaceutical Institute, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118 Kiel, Germany; (B.H.); (N.H.E.)
| | - Nathan Hugo Epalle
- Pharmaceutical Institute, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118 Kiel, Germany; (B.H.); (N.H.E.)
| | - Eric Beitz
- Pharmaceutical Institute, Christian-Albrechts-University of Kiel, Gutenbergstr. 76, 24118 Kiel, Germany; (B.H.); (N.H.E.)
- Correspondence: (E.B.); (S.H.)
| | - Stefan Hannus
- Intana Bioscience GmbH, Lochhamer Str. 29a, 82152 Planegg, Germany; (I.J.); (F.B.); (S.M.); (K.H.)
- Correspondence: (E.B.); (S.H.)
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Götz C, Hinze G, Gellert A, Maus H, von Hammerstein F, Hammerschmidt SJ, Lauth LM, Hellmich UA, Schirmeister T, Basché T. Conformational Dynamics of the Dengue Virus Protease Revealed by Fluorescence Correlation and Single-Molecule FRET Studies. J Phys Chem B 2021; 125:6837-6846. [PMID: 34137269 DOI: 10.1021/acs.jpcb.1c01797] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The dengue virus protease (DENV-PR) represents an attractive target for counteracting DENV infections. It is generally assumed that DENV-PR can exist in an open and a closed conformation and that active site directed ligands stabilize the closed state. While crystal structures of both the open and the closed conformation were successfully resolved, information about the prevalence of these conformations in solution remains elusive. Herein, we address the question of whether there is an equilibrium between different conformations in solution which can be influenced by addition of a competitive inhibitor. To this end, DENV-PR was statistically labeled by two dye molecules constituting a FRET (fluorescence resonance energy transfer) couple. Fluorescence correlation spectroscopy and photon-burst detection were employed to examine FRET pair labeled DENV-PRs freely diffusing in solution. The measurements were performed with two double mutants and with two dye couples. The data provide strong evidence that an equilibrium of at least two conformations of DENV-PR exists in solution. The competitive inhibitor stabilizes the closed state. Because the open and closed conformations appear to coexist in solution, our results support the picture of a conformational selection rather than that of an induced fit mechanism with respect to the inhibitor-induced formation of the closed state.
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Affiliation(s)
- Christian Götz
- Department of Chemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Gerald Hinze
- Department of Chemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Andrea Gellert
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Hannah Maus
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Franziska von Hammerstein
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Luca M Lauth
- Department of Chemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Ute A Hellmich
- Department of Chemistry, Johannes Gutenberg-University Mainz, Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Frankfurt, Germany
| | - Tanja Schirmeister
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Thomas Basché
- Department of Chemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
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α-Helical peptidic scaffolds to target α-synuclein toxic species with nanomolar affinity. Nat Commun 2021; 12:3752. [PMID: 34145261 PMCID: PMC8213730 DOI: 10.1038/s41467-021-24039-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/27/2021] [Indexed: 02/05/2023] Open
Abstract
α-Synuclein aggregation is a key driver of neurodegeneration in Parkinson's disease and related syndromes. Accordingly, obtaining a molecule that targets α-synuclein toxic assemblies with high affinity is a long-pursued objective. Here, we exploit the biophysical properties of toxic oligomers and amyloid fibrils to identify a family of α-helical peptides that bind to these α-synuclein species with low nanomolar affinity, without interfering with the monomeric functional protein. This activity is translated into a high anti-aggregation potency and the ability to abrogate oligomer-induced cell damage. Using a structure-guided search we identify a human peptide expressed in the brain and the gastrointestinal tract with analogous binding, anti-aggregation, and detoxifying properties. The chemical entities we describe here may represent a therapeutic avenue for the synucleinopathies and are promising tools to assist diagnosis by discriminating between native and toxic α-synuclein species.
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41
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Perrigue PM, Murray RA, Mielcarek A, Henschke A, Moya SE. Degradation of Drug Delivery Nanocarriers and Payload Release: A Review of Physical Methods for Tracing Nanocarrier Biological Fate. Pharmaceutics 2021; 13:770. [PMID: 34064155 PMCID: PMC8224277 DOI: 10.3390/pharmaceutics13060770] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/13/2022] Open
Abstract
Nanoformulations offer multiple advantages over conventional drug delivery, enhancing solubility, biocompatibility, and bioavailability of drugs. Nanocarriers can be engineered with targeting ligands for reaching specific tissue or cells, thus reducing the side effects of payloads. Following systemic delivery, nanocarriers must deliver encapsulated drugs, usually through nanocarrier degradation. A premature degradation, or the loss of the nanocarrier coating, may prevent the drug's delivery to the targeted tissue. Despite their importance, stability and degradation of nanocarriers in biological environments are largely not studied in the literature. Here we review techniques for tracing the fate of nanocarriers, focusing on nanocarrier degradation and drug release both intracellularly and in vivo. Intracellularly, we will discuss different fluorescence techniques: confocal laser scanning microscopy, fluorescence correlation spectroscopy, lifetime imaging, flow cytometry, etc. We also consider confocal Raman microscopy as a label-free technique to trace colocalization of nanocarriers and drugs. In vivo we will consider fluorescence and nuclear imaging for tracing nanocarriers. Positron emission tomography and single-photon emission computed tomography are used for a quantitative assessment of nanocarrier and payload biodistribution. Strategies for dual radiolabelling of the nanocarriers and the payload for tracing carrier degradation, as well as the efficacy of the payload delivery in vivo, are also discussed.
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Affiliation(s)
- Patrick M. Perrigue
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (P.M.P.); (A.M.); (A.H.)
| | - Richard A. Murray
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena S/N, 48940 Leioa, Spain;
| | - Angelika Mielcarek
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (P.M.P.); (A.M.); (A.H.)
| | - Agata Henschke
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (P.M.P.); (A.M.); (A.H.)
| | - Sergio E. Moya
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (P.M.P.); (A.M.); (A.H.)
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014 Donostia San Sebastián, Spain
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Affiliation(s)
- Yu Shi
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Peng
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Yang
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Zhao
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The University of Chinese Academy of Sciences, Beijing 100049, China
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Zorrilla S, Monterroso B, Robles-Ramos MÁ, Margolin W, Rivas G. FtsZ Interactions and Biomolecular Condensates as Potential Targets for New Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10030254. [PMID: 33806332 PMCID: PMC7999717 DOI: 10.3390/antibiotics10030254] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
FtsZ is an essential and central protein for cell division in most bacteria. Because of its ability to organize into dynamic polymers at the cell membrane and recruit other protein partners to form a “divisome”, FtsZ is a leading target in the quest for new antibacterial compounds. Strategies to potentially arrest the essential and tightly regulated cell division process include perturbing FtsZ’s ability to interact with itself and other divisome proteins. Here, we discuss the available methodologies to screen for and characterize those interactions. In addition to assays that measure protein-ligand interactions in solution, we also discuss the use of minimal membrane systems and cell-like compartments to better approximate the native bacterial cell environment and hence provide a more accurate assessment of a candidate compound’s potential in vivo effect. We particularly focus on ways to measure and inhibit under-explored interactions between FtsZ and partner proteins. Finally, we discuss recent evidence that FtsZ forms biomolecular condensates in vitro, and the potential implications of these assemblies in bacterial resistance to antibiotic treatment.
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Affiliation(s)
- Silvia Zorrilla
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Miguel-Ángel Robles-Ramos
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, TX 77030, USA;
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
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Schneider F, Sych T, Eggeling C, Sezgin E. Influence of nanobody binding on fluorescence emission, mobility, and organization of GFP-tagged proteins. iScience 2021; 24:101891. [PMID: 33364580 PMCID: PMC7753935 DOI: 10.1016/j.isci.2020.101891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/02/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022] Open
Abstract
Advanced fluorescence microscopy studies require specific and monovalent molecular labeling with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently labeled nanobodies against commonly employed fluorescent proteins (FPs). However, very little is known how these nanobodies influence their target molecules. Here, we tested commercially available nanobodies and observed clear changes of the fluorescence properties, mobility and organization of green fluorescent protein (GFP) tagged proteins after labeling with the anti-GFP nanobody. Intriguingly, we did not observe any co-diffusion of fluorescently labeled nanobodies with the GFP-labeled proteins. Our results suggest significant binding of the nanobodies to a non-emissive, likely oligomerized, form of the FPs, promoting disassembly into monomeric form after binding. Our findings have significant implications on the application of nanobodies and GFP labeling for studying dynamic and quantitative protein organization in the plasma membrane of living cells using advanced imaging techniques.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
- Jena Center of Soft Matters, Friedrich-Schiller-University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
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45
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Auer JMT, Stoddart JJ, Christodoulou I, Lima A, Skouloudaki K, Hall HN, Vukojević V, Papadopoulos DK. Of numbers and movement - understanding transcription factor pathogenesis by advanced microscopy. Dis Model Mech 2020; 13:dmm046516. [PMID: 33433399 PMCID: PMC7790199 DOI: 10.1242/dmm.046516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription factors (TFs) are life-sustaining and, therefore, the subject of intensive research. By regulating gene expression, TFs control a plethora of developmental and physiological processes, and their abnormal function commonly leads to various developmental defects and diseases in humans. Normal TF function often depends on gene dosage, which can be altered by copy-number variation or loss-of-function mutations. This explains why TF haploinsufficiency (HI) can lead to disease. Since aberrant TF numbers frequently result in pathogenic abnormalities of gene expression, quantitative analyses of TFs are a priority in the field. In vitro single-molecule methodologies have significantly aided the identification of links between TF gene dosage and transcriptional outcomes. Additionally, advances in quantitative microscopy have contributed mechanistic insights into normal and aberrant TF function. However, to understand TF biology, TF-chromatin interactions must be characterised in vivo, in a tissue-specific manner and in the context of both normal and altered TF numbers. Here, we summarise the advanced microscopy methodologies most frequently used to link TF abundance to function and dissect the molecular mechanisms underlying TF HIs. Increased application of advanced single-molecule and super-resolution microscopy modalities will improve our understanding of how TF HIs drive disease.
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Affiliation(s)
- Julia M T Auer
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Jack J Stoddart
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Ana Lima
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Hildegard N Hall
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Vladana Vukojević
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
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Pettersson P, Patrick J, Jakob M, Jacobs M, Klösgen RB, Wennmalm S, Mäler L. Soluble TatA forms oligomers that interact with membranes: Structure and insertion studies of a versatile protein transporter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183529. [PMID: 33279512 DOI: 10.1016/j.bbamem.2020.183529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/24/2023]
Abstract
The twin-arginine translocase (Tat) mediates the transport of already-folded proteins across membranes in bacteria, plants and archaea. TatA is a small, dynamic subunit of the Tat-system that is believed to be the active component during target protein translocation. TatA is foremost characterized as a bitopic membrane protein, but has also been found to partition into a soluble, oligomeric structure of yet unknown function. To elucidate the interplay between the membrane-bound and soluble forms we have investigated the oligomers formed by Arabidopsis thaliana TatA. We used several biophysical techniques to study the oligomeric structure in solution, the conversion that takes place upon interaction with membrane models of different compositions, and the effect on bilayer integrity upon insertion. Our results demonstrate that in solution TatA oligomerizes into large objects with a high degree of ordered structure. Upon interaction with lipids, conformational changes take place and TatA disintegrates into lower order oligomers. The insertion of TatA into lipid bilayers causes a temporary leakage of small molecules across the bilayer. The disruptive effect on the membrane is dependent on the liposome's negative surface charge density, with more leakage observed for purely zwitterionic bilayers. Overall, our findings indicate that A. thaliana TatA forms oligomers in solution that insert into bilayers, a process that involves reorganization of the protein oligomer.
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Affiliation(s)
- Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Joan Patrick
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mario Jakob
- Institut für Biologie, Institutsbereich Pflanzenphysiologie, Martin-Luther University, DE-06120 Halle-Wittenberg, Germany
| | - Malte Jacobs
- Institut für Biologie, Institutsbereich Pflanzenphysiologie, Martin-Luther University, DE-06120 Halle-Wittenberg, Germany
| | - Ralf Bernd Klösgen
- Institut für Biologie, Institutsbereich Pflanzenphysiologie, Martin-Luther University, DE-06120 Halle-Wittenberg, Germany
| | - Stefan Wennmalm
- Department of Applied Physics, Biophysics Group, Science for Life Laboratory, Royal Institute of Technology, Solna SE-171 65, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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Veerapathiran S, Teh C, Zhu S, Kartigayen I, Korzh V, Matsudaira PT, Wohland T. Wnt3 distribution in the zebrafish brain is determined by expression, diffusion and multiple molecular interactions. eLife 2020; 9:e59489. [PMID: 33236989 PMCID: PMC7725503 DOI: 10.7554/elife.59489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022] Open
Abstract
Wnt3 proteins are lipidated and glycosylated signaling molecules that play an important role in zebrafish neural patterning and brain development. However, the transport mechanism of lipid-modified Wnts through the hydrophilic extracellular environment for long-range action remains unresolved. Here we determine how Wnt3 accomplishes long-range distribution in the zebrafish brain. First, we characterize the Wnt3-producing source and Wnt3-receiving target regions. Subsequently, we analyze Wnt3 mobility at different length scales by fluorescence correlation spectroscopy and fluorescence recovery after photobleaching. We demonstrate that Wnt3 spreads extracellularly and interacts with heparan sulfate proteoglycans (HSPG). We then determine the binding affinity of Wnt3 to its receptor, Frizzled1 (Fzd1), using fluorescence cross-correlation spectroscopy and show that the co-receptor, low-density lipoprotein receptor-related protein 5 (Lrp5), is required for Wnt3-Fzd1 interaction. Our results are consistent with the extracellular distribution of Wnt3 by a diffusive mechanism that is modified by tissue morphology, interactions with HSPG, and Lrp5-mediated receptor binding, to regulate zebrafish brain development.
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Cathleen Teh
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shiwen Zhu
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Indira Kartigayen
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Paul T Matsudaira
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Thorsten Wohland
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
- Department of Chemistry, National University of SingaporeSingaporeSingapore
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48
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Single-molecule studies of amyloid proteins: from biophysical properties to diagnostic perspectives. Q Rev Biophys 2020; 53:e12. [PMID: 33148356 DOI: 10.1017/s0033583520000086] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In neurodegenerative diseases, a wide range of amyloid proteins or peptides such as amyloid-beta and α-synuclein fail to keep native functional conformations, followed by misfolding and self-assembling into a diverse array of aggregates. The aggregates further exert toxicity leading to the dysfunction, degeneration and loss of cells in the affected organs. Due to the disordered structure of the amyloid proteins, endogenous molecules, such as lipids, are prone to interact with amyloid proteins at a low concentration and influence amyloid cytotoxicity. The heterogeneity of amyloid proteinscomplicates the understanding of the amyloid cytotoxicity when relying only on conventional bulk and ensemble techniques. As complementary tools, single-molecule techniques (SMTs) provide novel insights into the different subpopulations of a heterogeneous amyloid mixture as well as the cytotoxicity, in particular as involved in lipid membranes. This review focuses on the recent advances of a series of SMTs, including single-molecule fluorescence imaging, single-molecule force spectroscopy and single-nanopore electrical recording, for the understanding of the amyloid molecular mechanism. The working principles, benefits and limitations of each technique are discussed and compared in amyloid protein related studies.. We also discuss why SMTs show great potential and are worthy of further investigation with feasibility studies as diagnostic tools of neurodegenerative diseases and which limitations are to be addressed.
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Sreenivasan VKA, Graus MS, Pillai RR, Yang Z, Goyette J, Gaus K. Influence of FRET and fluorescent protein maturation on the quantification of binding affinity with dual-channel fluorescence cross-correlation spectroscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:6137-6153. [PMID: 33282480 PMCID: PMC7687962 DOI: 10.1364/boe.401056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 06/12/2023]
Abstract
Protein-protein interactions at the plasma membrane mediate transmembrane signaling. Dual-channel fluorescence cross-correlation spectroscopy (dc-FCCS) is a method with which these interactions can be quantified in a cellular context. However, factors such as incomplete maturation of fluorescent proteins, spectral crosstalk, and fluorescence resonance energy transfer (FRET) affect quantification. Some of these can be corrected or accounted for during data analysis and/or interpretation. Here, we experimentally and analytically demonstrate that it is difficult to correct the error caused due to FRET when applying dc-FCCS to measure binding affinity or bound molecular concentrations. Additionally, the presence of dark fluorescent proteins due to incomplete maturation introduces further errors, which too cannot be corrected in the presence of FRET. Based on simulations, we find that modalities such as pulse-interleaved excitation FCCS do not eliminate FRET-induced errors. Finally, we demonstrate that the detrimental effect of FRET can be eliminated with careful experimental design when applying dc-FCCS to quantify protein-protein interactions at the plasma membrane of living cells.
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Affiliation(s)
- Varun K A Sreenivasan
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Matthew S Graus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Rashmi R Pillai
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Zhengmin Yang
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
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Wang H, Song S, Cheng H, Tan YW. State-of-the-Art Technologies for Understanding Brassinosteroid Signaling Networks. Int J Mol Sci 2020; 21:E8179. [PMID: 33142942 PMCID: PMC7662629 DOI: 10.3390/ijms21218179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/02/2023] Open
Abstract
Brassinosteroids, the steroid hormones of plants, control physiological and developmental processes through its signaling pathway. The major brassinosteroid signaling network components, from the receptor to transcription factors, have been identified in the past two decades. The development of biotechnologies has driven the identification of novel brassinosteroid signaling components, even revealing several crosstalks between brassinosteroid and other plant signaling pathways. Herein, we would like to summarize the identification and improvement of several representative brassinosteroid signaling components through the development of new technologies, including brassinosteroid-insensitive 1 (BRI1), BRI1-associated kinase 1 (BAK1), BR-insensitive 2 (BIN2), BRI1 kinase inhibitor 1 (BKI1), BRI1-suppressor 1 (BSU1), BR signaling kinases (BSKs), BRI1 ethyl methanesulfonate suppressor 1 (BES1), and brassinazole resistant 1 (BZR1). Furthermore, improvement of BR signaling knowledge, such as the function of BKI1, BES1 and its homologous through clustered regularly interspaced short palindromic repeats (CRISPR), the regulation of BIN2 through single-molecule methods, and the new in vivo interactors of BIN2 identified by proximity labeling are described. Among these technologies, recent advanced methods proximity labeling and single-molecule methods will be reviewed in detail to provide insights to brassinosteroid and other phytohormone signaling pathway studies.
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Affiliation(s)
- Haijiao Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475001, China;
| | - Song Song
- Department of Basic Courses, Zhejiang University of Water Resources and Electric Power, Hangzhou 310018, China;
| | - Huaqiang Cheng
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China;
| | - Yan-Wen Tan
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China;
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