1
|
Smith AW. Recent applications of fluorescence correlation spectroscopy in live cells. Curr Opin Chem Biol 2024; 81:102480. [PMID: 38905722 DOI: 10.1016/j.cbpa.2024.102480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
As a time-domain analogue of fluorescence imaging, FCS offers valuable insights into molecular dynamics, interactions, and concentrations within living cells. The primary insight generated by FCS is molecular mobility and concentration, which makes it useful for investigating molecular-scale details without the need for enrichment or separation. A specific strength of FCS is the ability to probe protein-protein interactions in live cells and several recent applications in this area are summarized. FCS is also used to investigate plasma membrane protein organization, with many applications to cell surface receptors and the mechanisms of drug binding. Finally, FCS is undergoing continual methodological innovations, such as imaging FCS, SPIM-FCS PIE-FCCS, STED-FCS, three-color FCS, and massively parallel FCS, which extend the capabilities to investigate molecular dynamics at different spatial and temporal scales. These innovations enable detailed examinations of cellular processes, including cellular transport and the spatial organization of membrane proteins.
Collapse
Affiliation(s)
- Adam W Smith
- Texas Tech University, Department of Chemistry & Biochemistry, Lubbock, TX, USA.
| |
Collapse
|
2
|
Choi AA, Xu K. Single-Molecule Diffusivity Quantification Unveils Ubiquitous Net Charge-Driven Protein-Protein Interaction. J Am Chem Soc 2024; 146:10973-10978. [PMID: 38576203 PMCID: PMC11023747 DOI: 10.1021/jacs.4c02475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Recent microscopy and nuclear magnetic resonance (NMR) studies have noticed substantial suppression of intracellular diffusion for positively charged proteins, suggesting an overlooked role of electrostatic attraction in nonspecific protein interactions in a predominantly negatively charged intracellular environment. Utilizing single-molecule detection and statistics, here, we quantify in aqueous solutions how protein diffusion, in the limit of low diffuser concentration to avoid aggregate/coacervate formation, is modulated by differently charged interactor proteins over wide concentration ranges. We thus report substantially suppressed diffusion when oppositely charged interactors are added at parts per million levels, yet unvaried diffusivities when same-charge interactors are added beyond 1%. The electrostatic attraction-driven suppression of diffusion is sensitive to the protein net charge states, as probed by varying the solution pH and ionic strength or chemically modifying the proteins and is robust across different diffuser-interactor pairs. By converting the measured diffusivities to diffuser diameters, we further show that in the limit of excess interactors, a positively charged diffuser molecule effectively drags along just one monolayer of negatively charged interactors, where further interactions stop. We thus unveil ubiquitous, net charge-driven protein-protein interactions and shed new light on the mechanism of charge-based diffusion suppression in living cells.
Collapse
Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
3
|
Mori I, Terasaka S, Yamaguchi S, Otosu T. Diffusion of Multiple Species Resolved by Fluorescence Lifetime Recovery after Photobleaching (FLRAP). Anal Chem 2024; 96:4854-4859. [PMID: 38497530 DOI: 10.1021/acs.analchem.3c05181] [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: 03/19/2024]
Abstract
Fluorescence recovery after photobleaching (FRAP) is now an indispensable tool to analyze the diffusion of molecules in vivo and in vitro. However, a conventional fluorescence intensity-based approach has difficulty in analyzing the diffusion of multiple species simultaneously. Here, we report fluorescence lifetime recovery after photobleaching (FLRAP) that incorporates fluorescence lifetime information into FRAP. By using FLRAP, the fluorescence intensity-recovery curves of each species can be successfully extracted from the ensemble photon data by utilizing their species-specific fluorescence decay curves, which are verified by applying FLRAP to two heterogeneous systems. Thus, FLRAP can be a powerful tool to quantitatively elucidate the molecular diffusion of multiple species in complex systems such as in living cells.
Collapse
Affiliation(s)
- Ikumi Mori
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Shun Terasaka
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| |
Collapse
|
4
|
Seltmann A, Carravilla P, Reglinski K, Eggeling C, Waithe D. Neural network informed photon filtering reduces fluorescence correlation spectroscopy artifacts. Biophys J 2024; 123:745-755. [PMID: 38384131 PMCID: PMC10995453 DOI: 10.1016/j.bpj.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/31/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Fluorescence correlation spectroscopy (FCS) techniques are well-established tools to investigate molecular dynamics in confocal and super-resolution microscopy. In practice, users often need to handle a variety of sample- or hardware-related artifacts, an example being peak artifacts created by bright, slow-moving clusters. Approaches to address peak artifacts exist, but measurements suffering from severe artifacts are typically nonanalyzable. Here, we trained a one-dimensional U-Net to automatically identify peak artifacts in fluorescence time series and then analyzed the purified, nonartifactual fluctuations by time-series editing. We show that, in samples with peak artifacts, the transit time and particle number distributions can be restored in simulations and validated the approach in two independent biological experiments. We propose that it is adaptable for other FCS artifacts, such as detector dropout, membrane movement, or photobleaching. In conclusion, this simulation-based, automated, open-source pipeline makes measurements analyzable that previously had to be discarded and extends every FCS user's experimental toolbox.
Collapse
Affiliation(s)
- Alexander Seltmann
- Institute for Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany; Leibniz Institute of Photonic Technology, Jena, Germany.
| | | | - Katharina Reglinski
- Institute for Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany; Leibniz Institute of Photonic Technology, Jena, Germany; Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany
| | - Christian Eggeling
- Institute for Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany; Leibniz Institute of Photonic Technology, Jena, Germany; Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany.
| | - Dominic Waithe
- MRC Centre for Computational Biology and Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| |
Collapse
|
5
|
Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
Collapse
Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
| |
Collapse
|
6
|
Yu W, Liu J, Huang X, Ren J. Study on Phase Separation of Fused in Sarcoma by Fluorescence Correlation Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1266-1276. [PMID: 38157426 DOI: 10.1021/acs.langmuir.3c02711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Liquid-liquid phase separation (LLPS) of fused in sarcoma (FUS) has emerged as a fundamental principle underpinning cellular function and malfunction. However, we know little about the FUS phase transition process from individual molecules to nanoscale condensates, which plays important roles in neurodegenerative diseases. Here, we propose the fluorescence correlation spectroscopy (FCS) method to quantitatively study the phase separation process of FUS protein with the fluorescent tag-enhanced green fluorescent protein (EGFP), from individual molecules to nanoscale condensates. The characteristic diffusion time (τD) of the protein condensates can be obtained from the FCS curve, which increases with the growth of the protein hydration radius. The bigger the τD value of the protein condensates, the larger the condensates formed by the phase separation of FUS. By this method, we discovered that the critical concentration for FUS to phase separation was 20 nM. We then plotted FUS phase diagrams based on τD under different concentrations of NaCl and found that both low-salt and high-salt concentrations tended to promote FUS-EGFP phase separation. Our results showed that ATP has a good inhibitory effect on FUS phase separation, and its inhibition constant IC50 was 3.2 mM. Finally, we evaluated the inhibition efficiency of single-stranded DNA sequences (ssDNA) on FUS phase separation and demonstrated that ssDNA containing three copies of TCCCCGT had relatively strong inhibition efficiency. In summary, our work provides detailed insight into the FUS phase transition process from individual molecules to nanoscale condensates at nanomolar concentrations and can be exploited for drug screening of neurodegenerative diseases.
Collapse
Affiliation(s)
- Wenxin Yu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Jian Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| |
Collapse
|
7
|
Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
Collapse
Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Larsen HA, Atkins WM, Nath A. The origins of nonideality exhibited by monoclonal antibodies and Fab fragments in human serum. Protein Sci 2023; 32:e4812. [PMID: 37861473 PMCID: PMC10659951 DOI: 10.1002/pro.4812] [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: 04/30/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
The development of therapeutic antibodies remains challenging, time-consuming, and expensive. A key contributing factor is a lack of understanding of how proteins are affected by complex biological environments such as serum and plasma. Nonideality due to attractive or repulsive interactions with cosolutes can alter the stability, aggregation propensity, and binding interactions of proteins in solution. Fluorescence correlation spectroscopy (FCS) can be used to measure apparent second virial coefficient (B2,app ) values for therapeutic and model monoclonal antibodies (mAbs) that capture the nature and strength of interactions with cosolutes directly in undiluted serum and similar complex biological media. Here, we use FCS-derived B2,app measurements to identify the components of human serum responsible for nonideal interactions with mAbs and Fab fragments. Most mAbs exhibit neutral or slightly attractive interactions with intact serum. Generally, mAbs display repulsive interactions with albumin and mildly attractive interactions with IgGs in the context of whole serum. Crucially, however, these attractive interactions are much stronger with pooled IgGs isolated from other serum components, indicating that the effects of serum nonideality can only be understood by studying the intact medium (rather than isolated components). Moreover, Fab fragments universally exhibited more attractive interactions than their parental mAbs, potentially rendering them more susceptible to nonideality-driven perturbations. FCS-based B2,app measurements have the potential to advance our understanding of how physiological environments impact protein-based therapeutics in general. Furthermore, incorporating such assays into preclinical biologics development may help de-risk molecules and make for a faster and more efficient development process.
Collapse
Affiliation(s)
- Hayli A. Larsen
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
| | - William M. Atkins
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Abhinav Nath
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
| |
Collapse
|
10
|
Schedler B, Yukhnovets O, Lindner L, Meyer A, Fitter J. The Thermodynamic Fingerprints of Ultra-Tight Nanobody-Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection. Int J Mol Sci 2023; 24:16379. [PMID: 38003569 PMCID: PMC10671529 DOI: 10.3390/ijms242216379] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Life on the molecular scale is based on a versatile interplay of biomolecules, a feature that is relevant for the formation of macromolecular complexes. Fluorescence-based two-color coincidence detection is widely used to characterize molecular binding and was recently improved by a brightness-gated version which gives more accurate results. We developed and established protocols which make use of coincidence detection to quantify binding fractions between interaction partners labeled with fluorescence dyes of different colors. Since the applied technique is intrinsically related to single-molecule detection, the concentration of diffusing molecules for confocal detection is typically in the low picomolar regime. This makes the approach a powerful tool for determining bi-molecular binding affinities, in terms of KD values, in this regime. We demonstrated the reliability of our approach by analyzing very strong nanobody-EGFP binding. By measuring the affinity at different temperatures, we were able to determine the thermodynamic parameters of the binding interaction. The results show that the ultra-tight binding is dominated by entropic contributions.
Collapse
Affiliation(s)
- Benno Schedler
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Olessya Yukhnovets
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Lennart Lindner
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Alida Meyer
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
| | - Jörg Fitter
- AG Biophysik, I. Physikalisches Institut (IA), RWTH Aachen University, 52074 Aachen, Germany; (B.S.); (O.Y.); (L.L.); (A.M.)
- ER-C-3 Structural Biology & IBI-6 Cellular Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
11
|
Dong C, Ren J. Resonance Light-Scattering Correlation Spectroscopy and Its Application in Analytical Chemistry for Life Science. Acc Chem Res 2023; 56:2582-2594. [PMID: 37706459 DOI: 10.1021/acs.accounts.3c00306] [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: 09/15/2023]
Abstract
Resonance light-scattering correlation spectroscopy (RLSCS) is a new single-particle detection method with its working principle being like fluorescence correlation spectroscopy (FCS). RLSCS is obtained by autocorrelation function analysis on the measured fluctuation of the resonance light scattering (RLS) intensity occurring within a subfemtoliter volume when a single nanoparticle (such as gold nanoparticles (NPs) or silver (SNPs)) freely diffuses through the volume. The RLSCS technique can detect such parameters as concentration, diffusion coefficient (translation and rotation), etc. Compared with the FCS technique, the correlated fluorescence intensity signal in RLSCS is replaced with the RLS signal of the nanoparticles, overcoming some limits of the fluorescent probes such as photobleaching under high-intensity or long-term illumination. In this Account, we showcase RLSCS methods, theoretical models at different optical configurations, and some key applications. First, the RLSCS optical detection system was constructed based on the confocal optics, its theoretical model was proposed, and the diffusion behaviors of the nanoparticles in the solution were studied including the rotational and translational diffusion. And, methods were developed to measure the concentration, size, aspect ratio, and size distribution of the NPs. Second, based on the RLSCS methods, some detection strategies were developed for homogeneous DNA detection, immunoassay, apoptosis assay, self-thermophoresis of the nanomotor, and quantitative assay in single living cells. Meanwhile, a new fluorescence/scattering cross-correlation spectroscopy (FSCCS) method was proposed for monitoring the molecule-particle interaction. This method enriched the conventional fluorescence/fluorescence cross-correlation spectroscopy (FCCS) method. Third, using the EMCCD with high sensitivity and rapid response as an optical detector, two temporospatially resolved scattering correlation spectroscopy methods and their theoretical models were developed: total internal reflection (TIR) configuration-based spatially resolved scattering correlation spectroscopy (SRSCS) and dark-field illumination-based scattering correlation spectroscopy (DFSCS). These methods extended single-spot confocal RLSCS to imaging RLSCS, which makes RLSCS have the ability for multiple channel detection with temporospatial resolution. The method was successfully used for investigating the dynamic behaviors of gold NPs in live cells and obtained its temporospatial concentration distribution and diffusion behaviors. The final section of this Account outlines future directions in the development of RLSCS.
Collapse
Affiliation(s)
- Chaoqing Dong
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| |
Collapse
|
12
|
Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
Collapse
Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
| |
Collapse
|
13
|
Chatterjee S, Kramer SN, Wellnitz B, Kim A, Kisley L. Spatially Resolving Size Effects on Diffusivity in Nanoporous Extracellular Matrix-like Materials with Fluorescence Correlation Spectroscopy Super-Resolution Optical Fluctuation Imaging. J Phys Chem B 2023; 127:4430-4440. [PMID: 37167609 DOI: 10.1021/acs.jpcb.3c00941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It is well documented that the nanoscale structures within porous microenvironments greatly impact the diffusion dynamics of molecules. However, how the interaction between the environment and molecules influences the diffusion dynamics has not been thoroughly explored. Here, we show that fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) can be used to accurately measure the diffusion dynamics of molecules within varying matrices such as nanopatterned surfaces and porous agarose hydrogels. Our data demonstrate the robustness of fcsSOFI, where it is possible not only to quantify the diffusion speeds of molecules in heterogeneous media but also to recover the matrix structure with resolution on the order of 100 nm. Using dextran molecules of varying sizes, we show that the diffusion coefficient is sensitive to the change in the molecular hydrodynamic radius. fcsSOFI images further reveal that smaller dextran molecules can freely move through the small pores of the hydrogel and report the detailed porous structure and local diffusion heterogeneities not captured by the average diffusion coefficient. Conversely, bigger dextran molecules are confined and unable to freely move through the hydrogel, highlighting only the larger pore structures. These findings establish fcsSOFI as a powerful tool to characterize spatial and diffusion information of diverse macromolecules within biorelevant matrices.
Collapse
Affiliation(s)
- Surajit Chatterjee
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Stephanie N Kramer
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Benjamin Wellnitz
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Albert Kim
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| |
Collapse
|
14
|
Choi AA, Xiang L, Li W, Xu K. Single-Molecule Displacement Mapping Indicates Unhindered Intracellular Diffusion of Small (≲1 kDa) Solutes. J Am Chem Soc 2023:10.1021/jacs.3c00597. [PMID: 37027457 PMCID: PMC10558625 DOI: 10.1021/jacs.3c00597] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
While fundamentally important, the intracellular diffusion of small (≲1 kDa) solutes has been difficult to elucidate due to challenges in both labeling and measurement. Here we quantify and spatially map the translational diffusion patterns of small solutes in mammalian cells by integrating several recent advances. In particular, by executing tandem stroboscopic illumination pulses down to 400 μs separation, we extend single-molecule displacement/diffusivity mapping (SMdM), a super-resolution diffusion quantification tool, to small solutes with high diffusion coefficients D of >300 μm2/s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ∼60-70% of that in vitro, up to ∼250 μm2/s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments.
Collapse
Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Limin Xiang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| |
Collapse
|
15
|
Park HH, Wang B, Moon S, Jepson T, Xu K. Machine-learning-powered extraction of molecular diffusivity from single-molecule images for super-resolution mapping. Commun Biol 2023; 6:336. [PMID: 36977778 PMCID: PMC10050076 DOI: 10.1038/s42003-023-04729-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
While critical to biological processes, molecular diffusion is difficult to quantify, and spatial mapping of local diffusivity is even more challenging. Here we report a machine-learning-enabled approach, pixels-to-diffusivity (Pix2D), to directly extract the diffusion coefficient D from single-molecule images, and consequently enable super-resolved D spatial mapping. Working with single-molecule images recorded at a fixed framerate under typical single-molecule localization microscopy (SMLM) conditions, Pix2D exploits the often undesired yet evident motion blur, i.e., the convolution of single-molecule motion trajectory during the frame recording time with the diffraction-limited point spread function (PSF) of the microscope. Whereas the stochastic nature of diffusion imprints diverse diffusion trajectories to different molecules diffusing at the same given D, we construct a convolutional neural network (CNN) model that takes a stack of single-molecule images as the input and evaluates a D-value as the output. We thus validate robust D evaluation and spatial mapping with simulated data, and with experimental data successfully characterize D differences for supported lipid bilayers of different compositions and resolve gel and fluidic phases at the nanoscale.
Collapse
Affiliation(s)
- Ha H Park
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Bowen Wang
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Suhong Moon
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA
| | - Tyler Jepson
- QB3-Berkeley, University of California, Berkeley, CA, 94720, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- QB3-Berkeley, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
16
|
Choi AA, Xiang L, Li W, Xu K. Single-molecule displacement mapping indicates unhindered intracellular diffusion of small (<~1 kDa) solutes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525579. [PMID: 36747694 PMCID: PMC9900885 DOI: 10.1101/2023.01.26.525579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
While fundamentally important, the intracellular diffusion of small (<~1 kDa) solutes has been difficult to elucidate due to challenges in both labeling and measurement. Here we quantify and spatially map the translational diffusion patterns of small solutes in mammalian cells by integrating several recent advances. In particular, by executing tandem stroboscopic illumination pulses down to 400-μs separation, we extend single-molecule displacement/diffusivity mapping (SM d M), a super-resolution diffusion quantification tool, to small solutes with high diffusion coefficients D of >300 μm 2 /s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ~60-70% of that in vitro , up to ~250 μm 2 /s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water, but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments. Abstract Graphic
Collapse
|
17
|
Balasubramanian H, Sankaran J, Pandey S, Goh CJH, Wohland T. The dependence of EGFR oligomerization on environment and structure: A camera-based N&B study. Biophys J 2022; 121:4452-4466. [PMID: 36335429 PMCID: PMC9748371 DOI: 10.1016/j.bpj.2022.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Number and brightness (N&B) analysis is a fluorescence spectroscopy technique to quantify oligomerization of the mobile fraction of proteins. Accurate results, however, rely on a good knowledge of nonfluorescent states of the fluorescent labels, especially of fluorescent proteins, which are widely used in biology. Fluorescent proteins have been characterized for confocal, but not camera-based, N&B, which allows, in principle, faster measurements over larger areas. Here, we calibrate camera-based N&B implemented on a total internal reflection fluorescence microscope for various fluorescent proteins by determining their propensity to be fluorescent. We then apply camera-based N&B in live CHO-K1 cells to determine the oligomerization state of the epidermal growth factor receptor (EGFR), a transmembrane receptor tyrosine kinase that is a crucial regulator of cell proliferation and survival with implications in many cancers. EGFR oligomerization in resting cells and its regulation by the plasma membrane microenvironment are still under debate. Therefore, we investigate the effects of extrinsic factors, including membrane organization, cytoskeletal structure, and ligand stimulation, and intrinsic factors, including mutations in various EGFR domains, on the receptor's oligomerization. Our results demonstrate that EGFR oligomerization increases with removal of cholesterol or sphingolipids or the disruption of GM3-EGFR interactions, indicating raft association. However, oligomerization is not significantly influenced by the cytoskeleton. Mutations in either I706/V948 residues or E685/E687/E690 residues in the kinase and juxtamembrane domains, respectively, lead to a decrease in oligomerization, indicating their necessity for EGFR dimerization. Finally, EGFR phosphorylation is oligomerization dependent, involving the extracellular domain (550-580 residues). Coupled with biochemical investigations, camera-based N&B indicates that EGFR oligomerization and phosphorylation are the outcomes of several molecular interactions involving the lipid content and structure of the cell membrane and multiple residues in the kinase, juxtamembrane, and extracellular domains.
Collapse
Affiliation(s)
- Harikrushnan Balasubramanian
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Jagadish Sankaran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shambhavi Pandey
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Corinna Jie Hui Goh
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
18
|
Correlated STORM-homoFRET imaging reveals highly heterogeneous membrane receptor structures. J Biol Chem 2022; 298:102448. [PMID: 36063991 PMCID: PMC9539790 DOI: 10.1016/j.jbc.2022.102448] [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: 12/20/2021] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Mapping the self-organization and spatial distribution of membrane proteins is key to understanding their function. Developing methods that can provide insight into correlations between membrane protein co-localization and interactions is challenging. We report here on a correlated stochastic optical reconstruction microscopy (STORM)/homoFRET imaging approach for resolving the nanoscale distribution and oligomeric state of membrane proteins. Using live cell homoFRET imaging of carcinoembryonic antigen-related cellular adhesion molecule (CEACAM1), a cell-surface receptor known to exist in a complex equilibrium between monomer and dimer/oligomer states, we revealed highly heterogeneous diffraction-limited structures on the surface of HeLa cells. Furthermore, correlated super-resolved STORM imaging showed that these structures comprised a complex mixture and spatial distribution of self-associated CEACAM1 molecules. In conclusion, this correlated approach provides a compelling strategy for addressing challenging questions about the interplay between membrane protein concentration, distribution, interaction, clustering, and function.
Collapse
|
19
|
Ng WS, Sielaff H, Zhao ZW. Phase Separation-Mediated Chromatin Organization and Dynamics: From Imaging-Based Quantitative Characterizations to Functional Implications. Int J Mol Sci 2022; 23:ijms23148039. [PMID: 35887384 PMCID: PMC9316379 DOI: 10.3390/ijms23148039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022] Open
Abstract
As an effective and versatile strategy to compartmentalize cellular components without the need for lipid membranes, phase separation has been found to underpin a wide range of intranuclear processes, particularly those involving chromatin. Many of the unique physico-chemical properties of chromatin-based phase condensates are harnessed by the cell to accomplish complex regulatory functions in a spatially and temporally controlled manner. Here, we survey key recent findings on the mechanistic roles of phase separation in regulating the organization and dynamics of chromatin-based molecular processes across length scales, packing states and intranuclear functions, with a particular emphasis on quantitative characterizations of these condensates enabled by advanced imaging-based approaches. By illuminating the complex interplay between chromatin and various chromatin-interacting molecular species mediated by phase separation, this review sheds light on an emerging multi-scale, multi-modal and multi-faceted landscape that hierarchically regulates the genome within the highly crowded and dynamic nuclear space. Moreover, deficiencies in existing studies also highlight the need for mechanism-specific criteria and multi-parametric approaches for the characterization of chromatin-based phase separation using complementary techniques and call for greater efforts to correlate the quantitative features of these condensates with their functional consequences in close-to-native cellular contexts.
Collapse
Affiliation(s)
- Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411, Singapore
- Correspondence:
| |
Collapse
|
20
|
Stoddart LA, Goulding J, Briddon SJ. Advances in the application of fluorescence correlation spectroscopy to study detergent purified and encapsulated membrane proteins. Int J Biochem Cell Biol 2022; 146:106210. [PMID: 35390493 DOI: 10.1016/j.biocel.2022.106210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a quantitative spectroscopy technique which could potentially increase throughput and sensitivity of screening for ligand, substrate and inhibitor binding to membrane proteins in solution. However, the purification of membrane proteins in their active forms is complex, as the lipid bilayer provides stability and its removal often causes the protein to become conformationally unstable. This has limited the application of biophysical techniques such as FCS to study the function of membrane proteins. The recent application of native extraction techniques such as styrene maleic acid lipid particles (SMALPs) has resolved this issue and FCS has emerged as a powerful option for studying proteins extracted in this way. This review will discuss the application of FCS to study purified membrane proteins in detergent micelles, nanodiscs and SMALPs and its potential to be used routinely in membrane protein drug discovery.
Collapse
Affiliation(s)
- Leigh A Stoddart
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK
| | - Joëlle Goulding
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK
| | - Stephen J Briddon
- Cell Signalling and Pharmacology Research Group, Division of Physiology Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, The Midlands, UK.
| |
Collapse
|
21
|
Markiewicz R, Litowczenko J, Gapiński J, Woźniak A, Jurga S, Patkowski A. Nanomolar Nitric Oxide Concentrations in Living Cells Measured by Means of Fluorescence Correlation Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031010. [PMID: 35164275 PMCID: PMC8838662 DOI: 10.3390/molecules27031010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023]
Abstract
Measurement of the nitric oxide (NO) concentration in living cells in the physiological nanomolar range is crucial in understanding NO biochemical functions, as well as in characterizing the efficiency and kinetics of NO delivery by NO-releasing drugs. Here, we show that fluorescence correlation spectroscopy (FCS) is perfectly suited for these purposes, due to its sensitivity, selectivity, and spatial resolution. Using the fluorescent indicators, diaminofluoresceins (DAFs), and FCS, we measured the NO concentrations in NO-producing living human primary endothelial cells, as well as NO delivery kinetics, by an external NO donor to the immortal human epithelial living cells. Due to the high spatial resolution of FCS, the NO concentration in different parts of the cells were also measured. The detection of nitric oxide by means of diaminofluoresceins is much more efficient and faster in living cells than in PBS solutions, even though the conversion to the fluorescent form is a multi-step reaction.
Collapse
Affiliation(s)
- Roksana Markiewicz
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
- Correspondence: (R.M.); (J.L.)
| | - Jagoda Litowczenko
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
- Correspondence: (R.M.); (J.L.)
| | - Jacek Gapiński
- Department of Molecular Biophysics, Faculty of Physics, Adam Mickiewicz University in Poznan, ul. Uniwersytetu Poznańskiego 3, 61-614 Poznan, Poland;
| | - Anna Woźniak
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland
| | - Stefan Jurga
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
| | - Adam Patkowski
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznan, Poland; (A.W.); (S.J.); (A.P.)
- Department of Molecular Biophysics, Faculty of Physics, Adam Mickiewicz University in Poznan, ul. Uniwersytetu Poznańskiego 3, 61-614 Poznan, Poland;
| |
Collapse
|
22
|
Slenders E, Perego E, Buttafava M, Tortarolo G, Conca E, Zappone S, Pierzynska-Mach A, Villa F, Petrini EM, Barberis A, Tosi A, Vicidomini G. Cooled SPAD array detector for low light-dose fluorescence laser scanning microscopy. BIOPHYSICAL REPORTS 2021; 1:None. [PMID: 34939046 PMCID: PMC8651514 DOI: 10.1016/j.bpr.2021.100025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/14/2021] [Indexed: 11/30/2022]
Abstract
The single-photon timing and sensitivity performance and the imaging ability of asynchronous-readout single-photon avalanche diode (SPAD) array detectors have opened up enormous perspectives in fluorescence (lifetime) laser scanning microscopy (FLSM), such as super-resolution image scanning microscopy and high-information content fluorescence fluctuation spectroscopy. However, the strengths of these FLSM techniques depend on the many different characteristics of the detector, such as dark noise, photon-detection efficiency, after-pulsing probability, and optical cross talk, whose overall optimization is typically a trade-off between these characteristics. To mitigate this trade-off, we present, to our knowledge, a novel SPAD array detector with an active cooling system that substantially reduces the dark noise without significantly deteriorating any other detector characteristics. In particular, we show that lowering the temperature of the sensor to −15°C significantly improves the signal/noise ratio due to a 10-fold decrease in the dark count rate compared with room temperature. As a result, for imaging, the laser power can be decreased by more than a factor of three, which is particularly beneficial for live-cell super-resolution imaging, as demonstrated in fixed and living cells expressing green-fluorescent-protein-tagged proteins. For fluorescence fluctuation spectroscopy, together with the benefit of the reduced laser power, we show that cooling the detector is necessary to remove artifacts in the correlation function, such as spurious negative correlations observed in the hot elements of the detector, i.e., elements for which dark noise is substantially higher than the median value. Overall, this detector represents a further step toward the integration of SPAD array detectors in any FLSM system.
Collapse
|
23
|
Dengue Virus Capsid-Protein Dynamics in Live Infected Cells Studied by Pair Correlation Analysis. Methods Mol Biol 2021. [PMID: 34709638 DOI: 10.1007/978-1-0716-1879-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
It has become increasingly evident that unveiling the mechanisms of virus entry, assembly, and virion release is fundamental for identifying means for preventing viral spread and controlling viral disease. Due to virus mobility and structural and/or functional heterogeneity among viral particles, high spatiotemporal resolution single-virus/single-particle techniques are required to capture the behavior of viral particles inside infected cells.In this chapter, we present fluorescence imaging analysis methods for studying the mobility of fluorescently labeled dengue virus (DENV) proteins in live infected cells. Some of the most recent Fluorescence Fluctuation Spectroscopy (FFS) methods will be presented and, in particular, the pair Correlation Functions (pCF) approach will be discussed. The pCF method does not require individual molecule isolation, as in a particle-tracking experiment, to capture single viral protein behavior. In this regard, image acquisition is followed by the spatiotemporal cross-correlation function at increasing time delays, yielding a quantitative view of single-particle mobility in intact live infected cells.We provide a general overview and a practical guidance for the implementation of advanced FFS techniques, and the pair Correlation Functions analysis, as quantitative tools to reveal insights into previously unreported DENV mechanisms. We expect this protocol report will serve as an incentive for further applying correlation imaging studies in virology research.
Collapse
|
24
|
Mateu-Regué À, Christiansen J, Bagger FO, Hellriegel C, Nielsen FC. Unveiling mRNP composition by fluorescence correlation and cross-correlation spectroscopy using cell lysates. Nucleic Acids Res 2021; 49:e119. [PMID: 34478550 PMCID: PMC8599746 DOI: 10.1093/nar/gkab751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 01/29/2023] Open
Abstract
Understanding the mRNA life cycle requires information about the dynamics and macromolecular composition and stoichiometry of mRNPs. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are appealing technologies to study these macromolecular structures because they have single molecule sensitivity and readily provide information about their molecular composition and dynamics. Here, we demonstrate how FCS can be exploited to study cytoplasmic mRNPs with high accuracy and reproducibility in cell lysates. Cellular lysates not only recapitulate data from live cells but provide improved readings and allow investigation of single mRNP analysis under particular conditions or following enzymatic treatments. Moreover, FCCS employing minute amounts of cells closely corroborated previously reported RNA dependent interactions and provided estimates of the relative overlap between factors in the mRNPs, thus depicting their heterogeneity. The described lysate-based FCS and FCCS analysis may not only complement current biochemical approaches but also provide novel opportunities for the quantitative analysis of the molecular composition and dynamics of single mRNPs.
Collapse
Affiliation(s)
- Àngels Mateu-Regué
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Jan Christiansen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Frederik Otzen Bagger
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Christian Hellriegel
- Carl Zeiss RMS / Harvard Center for Biological Imaging, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| |
Collapse
|
25
|
Kleczewska N, Sikorski PJ, Warminska Z, Markiewicz L, Kasprzyk R, Baran N, Kwapiszewska K, Karpinska A, Michalski J, Holyst R, Kowalska J, Jemielity J. Cellular delivery of dinucleotides by conjugation with small molecules: targeting translation initiation for anticancer applications. Chem Sci 2021; 12:10242-10251. [PMID: 34377411 PMCID: PMC8336483 DOI: 10.1039/d1sc02143e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Targeting cap-dependent translation initiation is one of the experimental approaches that could lead to the development of novel anti-cancer therapies. Synthetic dinucleoside 5',5'-triphosphates cap analogs are potent antagonists of eukaryotic translation initiation factor 4E (eIF4E) in vitro and could counteract elevated levels of eIF4E in cancer cells; however, transformation of these compounds into therapeutic agents remains challenging - they do not easily penetrate into cells and are susceptible to enzymatic cleavage. Here, we tested the potential of several small molecule ligands - folic acid, biotin, glucose, and cholesterol - to deliver both hydrolyzable and cleavage-resistant cap analogs into cells. A broad structure-activity relationship (SAR) study using model fluorescent probes and cap-ligand conjugates showed that cholesterol greatly facilitates uptake of cap analogs without disturbing the interactions with eIF4E. The most potent cholesterol conjugate identified showed apoptosis-mediated cytotoxicity towards cancer cells.
Collapse
Affiliation(s)
- Natalia Kleczewska
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Zofia Warminska
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Lukasz Markiewicz
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- Division of Biophysics Institute of Experimental Physics, Faculty of Physics University of Warsaw Pasteura 5 02-093 Warsaw Poland
| | - Natalia Baran
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
- Faculty of Biology University of Warsaw I. Miecznikowa 1 02-096 Warsaw Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Aneta Karpinska
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Jaroslaw Michalski
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Robert Holyst
- Institute of Physical Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Joanna Kowalska
- Division of Biophysics Institute of Experimental Physics, Faculty of Physics University of Warsaw Pasteura 5 02-093 Warsaw Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw Banacha 2c 02-097 Warsaw Poland
| |
Collapse
|
26
|
de Man SMA, Zwanenburg G, van der Wal T, Hink MA, van Amerongen R. Quantitative live-cell imaging and computational modeling shed new light on endogenous WNT/CTNNB1 signaling dynamics. eLife 2021; 10:e66440. [PMID: 34190040 PMCID: PMC8341982 DOI: 10.7554/elife.66440] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
WNT/CTNNB1 signaling regulates tissue development and homeostasis in all multicellular animals, but the underlying molecular mechanism remains incompletely understood. Specifically, quantitative insight into endogenous protein behavior is missing. Here, we combine CRISPR/Cas9-mediated genome editing and quantitative live-cell microscopy to measure the dynamics, diffusion characteristics and absolute concentrations of fluorescently tagged, endogenous CTNNB1 in human cells under both physiological and oncogenic conditions. State-of-the-art imaging reveals that a substantial fraction of CTNNB1 resides in slow-diffusing cytoplasmic complexes, irrespective of the activation status of the pathway. This cytoplasmic CTNNB1 complex undergoes a major reduction in size when WNT/CTNNB1 is (hyper)activated. Based on our biophysical measurements, we build a computational model of WNT/CTNNB1 signaling. Our integrated experimental and computational approach reveals that WNT pathway activation regulates the dynamic distribution of free and complexed CTNNB1 across different subcellular compartments through three regulatory nodes: the destruction complex, nucleocytoplasmic shuttling, and nuclear retention.
Collapse
Affiliation(s)
- Saskia MA de Man
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Gooitzen Zwanenburg
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Tanne van der Wal
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Mark A Hink
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
- van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| |
Collapse
|
27
|
Yao J, Huang X, Ren J. In situ determination of secretory kinase Fam20C from living cells using fluorescence correlation spectroscopy. Talanta 2021; 232:122473. [PMID: 34074441 DOI: 10.1016/j.talanta.2021.122473] [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: 01/31/2021] [Revised: 04/15/2021] [Accepted: 04/23/2021] [Indexed: 11/19/2022]
Abstract
Secretory proteins constitute a biologically crucial subset of proteins for regulation of some pathological and physiological processes, and they have become very important biomarkers in clinical diagnosis and therapeutic targets. So far, secretory protein functions and mechanisms have not been fully understood due to methodological limitations in detection of low-abundance proteins against medium background. Here, we propose a strategy to determine secretory protein from living cells in situ using fluorescence correlation spectroscopy (FCS). In this study, the recombinant protein Fam20C with SNAP-tag was used as a model protein, and O6-benzylguanine (BG) derivatives bearing fluorescent dye as probes. We synthesized three fluorescent probes and investigated their fluorescent properties and diffusion behaviors in solution, and found the probe BG-Bodipy-561 more suitable for in situ labeling of Fam20C. We confirmed the specific binding of the probe to the target protein by combining FCS and in-gel fluorescence scanning methods. We studied the effects of some factors of the secretory Fam20C, and found that RNA interference significantly inhibited the synthesis of secretory fused Fam20C, and myriocin had no significant effect on the expression of secretory Fam20C, which indirectly illustrated that sphingolipid signaling can regulate the Fam20C activity. We believe that FCS is a very promising method to analyze secretory proteins from living cells in situ.
Collapse
Affiliation(s)
- Jun Yao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Xiangyi Huang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| |
Collapse
|
28
|
Stapornwongkul KS, Vincent JP. Generation of extracellular morphogen gradients: the case for diffusion. Nat Rev Genet 2021; 22:393-411. [PMID: 33767424 DOI: 10.1038/s41576-021-00342-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Cells within developing tissues rely on morphogens to assess positional information. Passive diffusion is the most parsimonious transport model for long-range morphogen gradient formation but does not, on its own, readily explain scaling, robustness and planar transport. Here, we argue that diffusion is sufficient to ensure robust morphogen gradient formation in a variety of tissues if the interactions between morphogens and their extracellular binders are considered. A current challenge is to assess how the affinity for extracellular binders, as well as other biophysical and cell biological parameters, determines gradient dynamics and shape in a diffusion-based transport system. Technological advances in genome editing, tissue engineering, live imaging and in vivo biophysics are now facilitating measurement of these parameters, paving the way for mathematical modelling and a quantitative understanding of morphogen gradient formation and modulation.
Collapse
|
29
|
Li F, Du Z, Huang X, Dong C, Ren J. Analyses of p73 Protein Oligomerization and p73-MDM2 Interaction in Single Living Cells Using In Situ Single Molecule Spectroscopy. Anal Chem 2021; 93:886-894. [PMID: 33393764 DOI: 10.1021/acs.analchem.0c03521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein oligomerization and protein-protein interaction are crucial to regulate protein functions and biological processes. p73 protein is a very important transcriptional factor and can promote apoptosis and cell cycle arrest, and its transcriptional activity is regulated by p73 oligomerization and p73-MDM2 interaction. Although extracellular studies on p73 oligomerization and p73-MDM2 interaction have been carried out, it is unclear how p73 oligomerization and p73-MDM2 interaction occur in living cells. In our study, we described an in situ method for studying p73 oligomerization and p73-MDM2 interaction in living cells by combining fluorescence cross-correlation spectroscopy with a fluorescent protein labeling technique. Lentiviral transfection was used to transfect cells with a plasmid for either p73 or MDM2, each fused to a different fluorescent protein. p73 oligomerization was evaluated using brightness per particle, and the p73-MDM2 interaction was quantified using the cross-correlation value. We constructed a series of p73 mutants in three domains (transactivation domain, DNA binding domain, and oligomerization domain) and MDM2 mutants. We systematically studied p73 oligomerization and the effects of p73 oligomerization and the p73 and MDM2 structures on the p73-MDM2 interaction in single living cells. We have found that the p73 protein can form oligomers and that the p73 structure changes in the oligomerization domain significantly influence its oligomerization. p73 oligomerization and the structure changes significantly affect the p73-MDM2 interaction. Furthermore, the effects of inhibitors on p73 oligomerization and p73-MDM2 interaction were studied.
Collapse
Affiliation(s)
- Fucai Li
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Zhixue Du
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| |
Collapse
|
30
|
Harusawa K, Watanabe C, Kobori Y, Tomita K, Kitamura A, Kinjo M, Yanagisawa M. Membrane Surface Modulates Slow Diffusion in Small Crowded Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:437-444. [PMID: 33351626 DOI: 10.1021/acs.langmuir.0c03086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Membranes are ubiquitous structures in cells. The effects of membranes on various functional molecules have been reported, but their behaviors under macromolecular crowding and cell-sized confinement have not fully been understood. In this study, we model an intracellular environment by crowding micrometer-sized droplets and investigate the effects of membrane properties on molecular diffusion. The molecular diffusion inside small droplets covered with a lipid layer of phosphatidylcholine (PC) becomes slower compared with that of the corresponding bulk solutions under a crowding condition of polysaccharide dextran but not of its monomer unit, glucose. The addition of a poly(ethylene glycol) conjugated lipid (PEGylated lipid) to the PC membrane significantly alters the degree of slow diffusion observed inside small droplets of concentrated dextran. Interestingly, the change is not monotonic against dextran concentration; that is, the PEGylated membrane increases and decreases the degree of slow diffusion with increasing dextran concentration. We explain the nonmonotonic alternation from the increase in effective dextran concentration and the hindered temporal adsorption of dextran to the membrane. Because diffusion alteration by adding PEGylated lipid is observed for condensed small droplets of linear polymer PEG and hydrophilic protein bovine serum albumin, the phenomenon is general for other polymer systems as well. Furthermore, our findings may facilitate the understanding of intracellular molecular behaviors based on membrane effects as well as the development of numerous applications using polymer droplets.
Collapse
Affiliation(s)
- Kanae Harusawa
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Chiho Watanabe
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| | - Yuta Kobori
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Kazuho Tomita
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Akira Kitamura
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Masataka Kinjo
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Miho Yanagisawa
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Basic Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| |
Collapse
|
31
|
Yan R, Chen K, Xu K. Probing Nanoscale Diffusional Heterogeneities in Cellular Membranes through Multidimensional Single-Molecule and Super-Resolution Microscopy. J Am Chem Soc 2020; 142:18866-18873. [PMID: 33084318 DOI: 10.1021/jacs.0c08426] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diffusion properties notably determine the behavior of biomembranes. Here we report the concurrent nanoscale fine-mapping of membrane topography, diffusivity, and packing order in live mammalian cells through a synergy of single-molecule and super-resolution methods. By identifying a bright, lipophilic fluorescence turn-on probe that enables sustained single-molecule imaging of cellular membranes under stroboscopic excitation, we accumulate the positions and transient displacements of >106 probe molecules to achieve super-resolution topography and diffusivity mapping. We thus determine a trend that the membrane diffusivity drops with increased lipid packing order when comparing the endoplasmic reticulum (ER) membrane, plasma membrane, and nanodomains induced by cholera toxin B. Utilizing our nanoscale mapping capability, we further unveil reduced diffusivity in the ER membrane at ER-plasma membrane contact sites. By next integrating spectrally resolved single-molecule imaging, we show that this localized diffusion slowdown is not due to altered lipid packing order but may instead be attributed to local protein crowding. Our integrated multidimensional single-molecule approach thus unveils and differentiates between nanoscale diffusional heterogeneities of different origins in live-cell membranes.
Collapse
Affiliation(s)
- Rui Yan
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Kun Chen
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| |
Collapse
|
32
|
Pilz M, Kwapiszewska K, Kalwarczyk T, Bubak G, Nowis D, Hołyst R. Transport of nanoprobes in multicellular spheroids. NANOSCALE 2020; 12:19880-19887. [PMID: 32975267 DOI: 10.1039/d0nr01986k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The efficient delivery of drugs to cells depends on their diffusion through the extracellular matrix (ECM) of tissues. Here we present a study on the diffusion of nanoprobes of radius from 1 nm to over 100 nm in the ECM of spheroids of three cell types (HeLa, MCF-7 and fibroblasts). We quantified the nanoparticle transport in the spheroids' proliferating zone. We determined the size-dependent viscosity of the ECM. We revealed that nanoobjects up to 10 nm in radius exhibited unobstructed diffusion in the ECM, regardless of the spheroid type. The presented length-scale dependent viscosity profiles for spheroids pave the way for advanced modelling of drug administration through tissues.
Collapse
Affiliation(s)
- Marta Pilz
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Karina Kwapiszewska
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Tomasz Kalwarczyk
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Grzegorz Bubak
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Dominika Nowis
- Genomic Medicine, Medical University, Warsaw, Poland and Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, Poland
| | - Robert Hołyst
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| |
Collapse
|
33
|
Grime RL, Goulding J, Uddin R, Stoddart LA, Hill SJ, Poyner DR, Briddon SJ, Wheatley M. Single molecule binding of a ligand to a G-protein-coupled receptor in real time using fluorescence correlation spectroscopy, rendered possible by nano-encapsulation in styrene maleic acid lipid particles. NANOSCALE 2020; 12:11518-11525. [PMID: 32428052 DOI: 10.1039/d0nr01060j] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The fundamental importance of membrane proteins in cellular processes has driven a marked increase in the use of membrane mimetic approaches for studying and exploiting these proteins. Nano-encapsulation strategies which preserve the native lipid bilayer environment are particularly attractive. Consequently, the use of poly(styrene co-maleic acid) (SMA) has been widely adopted to solubilise proteins directly from cell membranes by spontaneously forming "SMA Lipid Particles" (SMALPs). G-protein-coupled receptors (GPCRs) are ubiquitous "chemical switches", are central to cell signalling throughout the evolutionary tree, form the largest family of membrane proteins in humans and are a major drug discovery target. GPCR-SMALPs that retain binding capability would be a versatile platform for a wide range of down-stream applications. Here, using the adenosine A2A receptor (A2AR) as an archetypical GPCR, we show for the first time the utility of fluorescence correlation spectroscopy (FCS) to characterise the binding capability of GPCRs following nano-encapsulation. Unbound fluorescent ligand CA200645 exhibited a monophasic autocorrelation curve (dwell time, τD = 68 ± 2 μs; diffusion coefficient, D = 287 ± 15 μm2 s-1). In the presence of A2AR-SMALP, bound ligand was also evident (τD = 625 ± 23 μs; D = 30 ± 4 μm2 s-1). Using a non-receptor control (ZipA-SMALP) plus competition binding confirmed that this slower component represented binding to the encapsulated A2AR. Consequently, the combination of GPCR-SMALP and FCS is an effective platform for the quantitative real-time characterisation of nano-encapsulated receptors, with single molecule sensitivity, that will have widespread utility for future exploitation of GPCR-SMALPs in general.
Collapse
Affiliation(s)
- Rachael L Grime
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Joelle Goulding
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Romez Uddin
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Leigh A Stoddart
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Stephen J Hill
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David R Poyner
- Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | - Stephen J Briddon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mark Wheatley
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK and Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Alison Gingell Building, Coventry University, Coventry, CV1 2DS, UK.
| |
Collapse
|
34
|
Gabriel M, Navarro GSC, de Borba L, Rossi AH, Gamarnik AV, Estrada LC. Dengue Virus Capsid Protein Dynamics Reveals Spatially Heterogeneous Motion in Live-Infected-Cells. Sci Rep 2020; 10:8751. [PMID: 32472078 PMCID: PMC7260208 DOI: 10.1038/s41598-020-65625-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/05/2020] [Indexed: 11/15/2022] Open
Abstract
Dengue is the single most important human viral infection transmitted by insects. The function of the viral proteins andtheir interactions with the host cell is under exhaustive investigation with the aim of identifying antiviral strategies. Here,using recombinant full-length dengue virus genomes, carrying a fluorescent mCherry fused to capsid, we studied biophysicalproperties of the viral protein during one infectious cycle in living cells. Dengue virus capsid protein associates to differentcellular compartments but its function in these locations is largely unknown. We evaluated the diffusion of capsid inside the celland determined a higher effective diffusion coefficient in the cytoplasm than in the nucleus. Using advanced fluorescencecorrelation methods, including the recently developed two-dimensional pair correlation analysis, we constructed for the first timehigh resolution maps of capsid mobility in an infected cell. We observed that the motion of capsid in the nucleoplasm-nucleolusinterface was highly organized, indicating an obstacle in this interface. Although nucleoli are membraneless structures, theydisplayed liquid-liquid phase separation. Once inside nucleoli, the protein showed isotropic mobility, indicating free diffusion orimmobilized capsid inside these structures. This is the first study presenting spatial and temporal dynamics of the dengue viruscapsid protein during infection.
Collapse
Affiliation(s)
- Manuela Gabriel
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), Buenos Aires, 1428, Argentina
| | - Guadalupe S Costa Navarro
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Luana de Borba
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Andrés H Rossi
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Andrea V Gamarnik
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Laura C Estrada
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), Buenos Aires, 1428, Argentina.
| |
Collapse
|
35
|
Zhang H, Rombouts K, Raes L, Xiong R, De Smedt SC, Braeckmans K, Remaut K. Fluorescence-Based Quantification of Messenger RNA and Plasmid DNA Decay Kinetics in Extracellular Biological Fluids and Cell Extracts. ACTA ACUST UNITED AC 2020; 4:e2000057. [PMID: 32402121 DOI: 10.1002/adbi.202000057] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022]
Abstract
Extracellular and intracellular degradation of nucleic acids remains an issue in non-viral gene therapy. Understanding biodegradation is critical for the rational design of gene therapeutics in order to maintain stability and functionality at the target site. However, there are only limited methods available that allow determining the stability of genetic materials in biological environments. In this context, the decay kinetics of fluorescently labeled plasmid DNA (pDNA) and messenger RNA (mRNA) in undiluted biological samples (i.e., human serum, human ascites, bovine vitreous) and cell extracts is studied using fluorescence correlation spectroscopy (FCS) and single particle tracking (SPT). It is demonstrated that FCS is suitable to follow mRNA degradation, while SPT is better suited to investigate pDNA integrity. The half-life of mRNA and pDNA is ≈1-2 min and 1-4 h in biological samples, respectively. The resistance against biodegradation drastically improves by complexation with lipid-based carriers. Taken together, FCS and SPT are able to quantify the integrity of mRNA and pDNA, respectively, as a function of time, both in the extracellular biological fluids and cell extracts. This in turn allows to focus on the important but less understood issue of nucleic acids degradation in more detail and to rationally optimize gene delivery system as therapeutics.
Collapse
Affiliation(s)
- Heyang Zhang
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Koen Rombouts
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Laurens Raes
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Ranhua Xiong
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| | - Katrien Remaut
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, 9000, Belgium
| |
Collapse
|
36
|
Single-molecule displacement mapping unveils nanoscale heterogeneities in intracellular diffusivity. Nat Methods 2020; 17:524-530. [PMID: 32203387 PMCID: PMC7205592 DOI: 10.1038/s41592-020-0793-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/14/2020] [Indexed: 11/08/2022]
Abstract
Intracellular diffusion underlies vital cellular processes. However, it remains difficult to elucidate how an unbound protein diffuses inside the cell with good spatial resolution and sensitivity. Here we introduce single-molecule displacement/diffusivity mapping (SMdM), a super-resolution strategy that enables the nanoscale mapping of intracellular diffusivity through local statistics of the instantaneous displacements of freely diffusing single molecules. We thus show that the diffusion of an average-sized protein in the mammalian cytoplasm and nucleus is spatially heterogeneous at the nanoscale, and that variations in local diffusivity correlate with the ultrastructure of the actin cytoskeleton and the organization of the genome, respectively. SMdM of differently charged proteins further unveils that the possession of positive, but not negative, net charges drastically impedes diffusion, and that the rate is determined by the specific subcellular environments. We thus unveil rich heterogeneities and charge effects in intracellular diffusion at the nanoscale.
Collapse
|
37
|
Watanabe C, Kobori Y, Yamamoto J, Kinjo M, Yanagisawa M. Quantitative Analysis of Membrane Surface and Small Confinement Effects on Molecular Diffusion. J Phys Chem B 2020; 124:1090-1098. [PMID: 31939302 DOI: 10.1021/acs.jpcb.9b10558] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular behaviors in small liquid droplets (picoliter scale), such as phase transitions and chemical reactions, are essential for the industrial application of small droplets and their use as artificial cells. However, the droplets often differ from those in bulk solutions (milliliter scale). Since the droplet size is much larger than the molecular size, the so-called size effect that draws these differences has attracted attention as a target to be solved. Although the small volume and the membrane surface surrounding the droplet are thought to be the origin of the size effect, there were little attempts to separate and quantify them. To solve the problem, we develop a series of systems for the evaluation. Using these systems, we have evaluated the size effect of concentrated polymer solutions on molecular diffusion by dividing it into small volume and membrane surface contributions. Our results demonstrate that the size effect on the molecular diffusion originates from the long-range interaction with the surface enhanced with decreasing volume. The quantitative size effect revealed by the systems provides novel insights in the biophysical understanding of molecular behaviors in cells and to the regulation and design of micrometer-sized materials.
Collapse
Affiliation(s)
- Chiho Watanabe
- Komaba Institute for Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan
| | - Yuta Kobori
- Komaba Institute for Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan.,Department of Applied Physics , Tokyo University of Agriculture and Technology , Naka-cho 2-24-16 , Koganei , Tokyo 184-8588 , Japan
| | - Johtaro Yamamoto
- Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Central 6, Higashi 1-1-1 , Tsukuba , Ibaraki 305-8568 , Japan
| | - Masataka Kinjo
- Faculty of Advanced Life Science , Hokkaido University , Kita-21 Nishi-11 Kita-ku , Sapporo , Hokkaido 001-0021 , Japan
| | - Miho Yanagisawa
- Komaba Institute for Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan.,Department of Basic Science , The University of Tokyo , Komaba 3-8-1 , Meguro , Tokyo 153-8902 , Japan
| |
Collapse
|
38
|
Yu S, Li F, Huang X, Dong C, Ren J. In Situ Study of Interactions between Endogenous c-myc mRNA with CRDBP in a Single Living Cell by Combining Fluorescence Cross-Correlation Spectroscopy with Molecular Beacons. Anal Chem 2020; 92:2988-2996. [DOI: 10.1021/acs.analchem.9b03934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- 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
| | - Fucai Li
- 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
| | - 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
| | - 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
| |
Collapse
|
39
|
Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
Collapse
Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
| |
Collapse
|
40
|
Li Y, Wang M, Tao Y, Zhang R, Zhou M, Tao P, Feng P, Huang W, Huang H, Miao W. Highly stable and biocompatible nanocontrast agent encapsulating a novel organic fluorescent dye for enhanced cellular imaging. POWDER TECHNOL 2019. [DOI: 10.1016/j.powtec.2018.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
41
|
Di Silvio D, Martínez-Moro M, Salvador C, de Los Angeles Ramirez M, Caceres-Velez PR, Ortore MG, Dupin D, Andreozzi P, Moya SE. Self-assembly of poly(allylamine)/siRNA nanoparticles, their intracellular fate and siRNA delivery. J Colloid Interface Sci 2019; 557:757-766. [PMID: 31569055 DOI: 10.1016/j.jcis.2019.09.082] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/17/2019] [Accepted: 09/21/2019] [Indexed: 12/18/2022]
Abstract
Silencing RNA (siRNA) technologies attract significant interest as a therapeutic tool for a large number of diseases. However, the medical translation of this technology is hampered by the lack of effective delivery vehicles for siRNAs in cytosol that prevent their degradation in the bloodstream. The use of molecular complexes based on polyamines have great potential for siRNA delivery as polyamines can protect the siRNA during circulation and at the same time favor siRNA translocation in cytosol. Here, nanoparticles are prepared by complexation of poly(allylamine hydrochloride) (PAH) and siRNA varying the ratio of nitrogen groups from PAH to phosphate groups from siRNA (N/P ratio). Nanoparticles are characterized by transmission electron microscopy and dynamic light scattering. The stability of complexes of green rhodamine labelled PAH (G-PAH) and Cy5 labelled siRNA (R-siRNA) at different pHs and in cell media is studied by fluorescence cross-correlation spectroscopy (FCCS). FCCS studies show that the nanoparticles are stable at physiological pH and in cell media but they disassemble at acidic pH. An optimal N/P ratio of 2 is identified in terms of stability in media, degradation at endosomal pH and toxicity. The intracellular fate of the complexes is studied following uptake in A549 cells. The cross-correlation between G-PAH and R-siRNA decreases substantially 24 h after uptake, while diffusion times of siRNA decrease indicating that the complexes disassemble, liberating the siRNAs. The release of siRNAs into the cytosol is confirmed with parallel confocal laser scanning microscopy. Flow cytometry studies show that PAH/siRNA nanoparticles are effective at silencing green fluorescent protein expression at low N/P ratios at which polyethylenimine/siRNA shows no significant silencing.
Collapse
Affiliation(s)
- Desirè Di Silvio
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain
| | - Marta Martínez-Moro
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain
| | - Cristian Salvador
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain; CIDETEC Nanomedicine, Paseo Miramón, 196, 20014 Donostia-San Sebastián, Spain
| | - Maria de Los Angeles Ramirez
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain; Instituto de Nanosistemas, Universidad Nacional de San Martín (INS-UNSAM), Av. 25 de Mayo 1021, San Martín, Buenos Aires, Argentina
| | - Paolin Rocio Caceres-Velez
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain
| | - Maria Grazia Ortore
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Damien Dupin
- CIDETEC Nanomedicine, Paseo Miramón, 196, 20014 Donostia-San Sebastián, Spain
| | - Patrizia Andreozzi
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain.
| | - Sergio E Moya
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain.
| |
Collapse
|
42
|
Abstract
Understanding the cellular basis of human health and disease requires the spatial resolution of microscopy and the molecular-level details provided by spectroscopy. This review highlights imaging methods at the intersection of microscopy and spectroscopy with applications in cell biology. Imaging methods are divided into three broad categories: fluorescence microscopy, label-free approaches, and imaging tools that can be applied to multiple imaging modalities. Just as these imaging methods allow researchers to address new biological questions, progress in biological sciences will drive the development of new imaging methods. We highlight four topics in cell biology that illustrate the need for new imaging tools: nanoparticle-cell interactions, intracellular redox chemistry, neuroscience, and the increasing use of spheroids and organoids. Overall, our goal is to provide a brief overview of individual imaging methods and highlight recent advances in the use of microscopy for cell biology.
Collapse
Affiliation(s)
- Joshua D Morris
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, Georgia 30043, USA
| | - Christine K Payne
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA;
| |
Collapse
|
43
|
Struk S, Jacobs A, Sánchez Martín-Fontecha E, Gevaert K, Cubas P, Goormachtig S. Exploring the protein-protein interaction landscape in plants. PLANT, CELL & ENVIRONMENT 2019; 42:387-409. [PMID: 30156707 DOI: 10.1111/pce.13433] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 05/24/2023]
Abstract
Protein-protein interactions (PPIs) represent an essential aspect of plant systems biology. Identification of key protein players and their interaction networks provide crucial insights into the regulation of plant developmental processes and into interactions of plants with their environment. Despite the great advance in the methods for the discovery and validation of PPIs, still several challenges remain. First, the PPI networks are usually highly dynamic, and the in vivo interactions are often transient and difficult to detect. Therefore, the properties of the PPIs under study need to be considered to select the most suitable technique, because each has its own advantages and limitations. Second, besides knowledge on the interacting partners of a protein of interest, characteristics of the interaction, such as the spatial or temporal dynamics, are highly important. Hence, multiple approaches have to be combined to obtain a comprehensive view on the PPI network present in a cell. Here, we present the progress in commonly used methods to detect and validate PPIs in plants with a special emphasis on the PPI features assessed in each approach and how they were or can be used for the study of plant interactions with their environment.
Collapse
Affiliation(s)
- Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Elena Sánchez Martín-Fontecha
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| |
Collapse
|
44
|
Yu S, Du Z, Dong C, Ren J. In situ study of RSK2 kinase activity in a single living cell by combining single molecule spectroscopy with activity-based probes. Analyst 2019; 144:3756-3764. [DOI: 10.1039/c9an00178f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FCS with the ABP strategy is a very promising method for studying endogenous protein kinases in living cells.
Collapse
Affiliation(s)
- Shengrong Yu
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Zhixue Du
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| |
Collapse
|
45
|
Titeca K, Lemmens I, Tavernier J, Eyckerman S. Discovering cellular protein-protein interactions: Technological strategies and opportunities. MASS SPECTROMETRY REVIEWS 2019; 38:79-111. [PMID: 29957823 DOI: 10.1002/mas.21574] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 01/03/2018] [Accepted: 06/04/2018] [Indexed: 05/09/2023]
Abstract
The analysis of protein interaction networks is one of the key challenges in the study of biology. It connects genotypes to phenotypes, and disruption often leads to diseases. Hence, many technologies have been developed to study protein-protein interactions (PPIs) in a cellular context. The expansion of the PPI technology toolbox however complicates the selection of optimal approaches for diverse biological questions. This review gives an overview of the binary and co-complex technologies, with the former evaluating the interaction of two co-expressed genetically tagged proteins, and the latter only needing the expression of a single tagged protein or no tagged proteins at all. Mass spectrometry is crucial for some binary and all co-complex technologies. After the detailed description of the different technologies, the review compares their unique specifications, advantages, disadvantages, and applicability, while highlighting opportunities for further advancements.
Collapse
Affiliation(s)
- Kevin Titeca
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Irma Lemmens
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| |
Collapse
|
46
|
Bouchaala R, Richert L, Anton N, Vandamme TF, Djabi S, Mély Y, Klymchenko AS. Quantifying Release from Lipid Nanocarriers by Fluorescence Correlation Spectroscopy. ACS OMEGA 2018; 3:14333-14340. [PMID: 30411065 PMCID: PMC6210065 DOI: 10.1021/acsomega.8b01488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
Understanding the release of drugs and contrast agents from nanocarriers is fundamental in the development of new effective nanomedicines. However, the commonly used method based on dialysis frequently fails to quantify the release of molecules poorly soluble in water, and it is not well-suited for in situ measurements in biological media. Here, we have developed a new methodology for quantifying the release of fluorescent molecules from lipid nanocarriers (LNCs) using fluorescence correlation spectroscopy (FCS). LNCs based on nanoemulsion droplets, encapsulating the hydrophobic Nile red derivative NR668 as a model cargo, were used. Our studies revealed that the standard deviation of fluorescence fluctuations in FCS measurements depends linearly on the dye loading in the nanocarriers, and it is insensitive to the presence of less-bright molecular emissive species in solution. In sharp contrast, classical FCS parameters, such as the number and the brightness of emissive species, are strongly influenced by the fluorescence of molecular species in solution. Therefore, we propose to use the standard deviation of fluorescence fluctuations for the quantitative analysis of dye release from nanocarriers, which is unaffected by the "parasite" fluorescence of the released dyes or the auto-fluorescence of the medium. Using this method, we found that LNCs remain intact in water, whereas in serum medium, they release their content in a temperature-dependent manner. At 37 °C, the release was relatively slow reaching 50% only after 6 h of incubation. The results are corroborated by qualitative observations based on Förster resonance energy transfer between two different encapsulated dyes. The developed method is simple because it is only based on the standard deviation of fluorescence fluctuations and, in principle, can be applied to nanocarriers of different types.
Collapse
Affiliation(s)
- Redouane Bouchaala
- CNRS
UMR 7021, Laboratoire de Bioimagerie et Pathologies, University of
Strasbourg, 67401 Illkirch Cedex, France
- Laboratory
of Photonic Systems and Nonlinear Optics, Institute of Optics and
Fine Mechanics, University of Setif 1, 19000 Setif, Algeria
| | - Ludovic Richert
- CNRS
UMR 7021, Laboratoire de Bioimagerie et Pathologies, University of
Strasbourg, 67401 Illkirch Cedex, France
| | - Nicolas Anton
- CNRS
UMR 7199, Laboratoire de Conception et Application de Molécules
Bioactives, University of Strasbourg, 67401 Illkirch Cedex, France
| | - Thierry F. Vandamme
- CNRS
UMR 7199, Laboratoire de Conception et Application de Molécules
Bioactives, University of Strasbourg, 67401 Illkirch Cedex, France
| | - Smail Djabi
- Laboratory
of Photonic Systems and Nonlinear Optics, Institute of Optics and
Fine Mechanics, University of Setif 1, 19000 Setif, Algeria
| | - Yves Mély
- CNRS
UMR 7021, Laboratoire de Bioimagerie et Pathologies, University of
Strasbourg, 67401 Illkirch Cedex, France
| | - Andrey S. Klymchenko
- CNRS
UMR 7021, Laboratoire de Bioimagerie et Pathologies, University of
Strasbourg, 67401 Illkirch Cedex, France
| |
Collapse
|
47
|
Wijesooriya CS, Nyamekye CKA, Smith EA. Optical Imaging of the Nanoscale Structure and Dynamics of Biological Membranes. Anal Chem 2018; 91:425-440. [DOI: 10.1021/acs.analchem.8b04755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Charles K. A. Nyamekye
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| | - Emily A. Smith
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
- The Ames Laboratory, U.S. Department of Energy, Ames, Iowa 50011, United States
| |
Collapse
|
48
|
Zheng Y, Xu L, Yang J, Peng X, Wang H, Yu N, Hua Y, Zhao J, He J, Hong T. The effects of fluorescent labels on Aβ42
aggregation detected by fluorescence correlation spectroscopy. Biopolymers 2018; 109:e23237. [DOI: 10.1002/bip.23237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 09/02/2018] [Accepted: 09/13/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Yanpeng Zheng
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Lingwan Xu
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Jingfa Yang
- Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Xianglei Peng
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - He Wang
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Na Yu
- School of Sciences; Beijing Jiaotong University; Beijing China
- Shandong Xinchuang Biological Technology Co., Ltd.; Jinan China
| | - Ying Hua
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Jiang Zhao
- Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Jinsheng He
- School of Sciences; Beijing Jiaotong University; Beijing China
| | - Tao Hong
- School of Sciences; Beijing Jiaotong University; Beijing China
- Institute for Viral Disease Control and Prevention; Chinese Centre for Disease Control and Prevention; Beijing China
| |
Collapse
|
49
|
Garni M, Einfalt T, Goers R, Palivan CG, Meier W. Live Follow-Up of Enzymatic Reactions Inside the Cavities of Synthetic Giant Unilamellar Vesicles Equipped with Membrane Proteins Mimicking Cell Architecture. ACS Synth Biol 2018; 7:2116-2125. [PMID: 30145889 DOI: 10.1021/acssynbio.8b00104] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Compartmentalization of functional biological units, cells, and organelles serves as an inspiration for the development of biomimetic materials with unprecedented properties and applications in biosensing and medicine. Because of the complexity of cells, the design of ideal functional materials remains a challenge. An elegant strategy to obtain cell-like compartments as novel materials with biofunctionality is the combination of synthetic micrometer-sized giant unilamellar vesicles (GUVs) with biomolecules because it enables studying the behavior of biomolecules and processes within confined cavities. Here we introduce a functional cell-mimetic compartment formed by insertion of the model biopore bacterial membrane protein OmpF in thick synthetic membranes of an artificial GUV compartment that encloses-as a model-the oxidative enzyme horseradish peroxidase. In this manner, a simple and robust cell mimic is designed: the biopore serves as a gate that allows substrates to enter cavities of the GUVs, where they are converted into products by the encapsulated enzyme and then released in the environments of GUVs. Our bioequipped GUVs facilitate the control of specific catalytic reactions in confined microscale spaces mimicking cell size and architecture and thus provide a straightforward approach serving to obtain deeper insights into biological processes inside cells in real time.
Collapse
Affiliation(s)
- Martina Garni
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002 Basel, Switzerland
| | - Tomaz Einfalt
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002 Basel, Switzerland
| | - Roland Goers
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Cornelia G. Palivan
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002 Basel, Switzerland
| | - Wolfgang Meier
- Department of Chemistry, University of Basel, Mattenstrasse 24a, CH-4002 Basel, Switzerland
| |
Collapse
|
50
|
Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
Collapse
Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
| |
Collapse
|