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Liu J, Yu W, Dong C, Huang X, Ren J. Objective scanning-based fluorescence cross-correlation spectroscopy (Scan-FCCS) for studying the fusion dynamics of protein phase separation. Analyst 2024; 149:2719-2727. [PMID: 38525957 DOI: 10.1039/d4an00264d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Protein phase separation plays a very important role in many biological processes and is closely related to the occurrence and development of some serious diseases. So far, the fluorescence imaging method and fluorescence correlation spectroscopy (FCS) have been frequently used to study the phase separation behavior of proteins. Due to the wide size distribution of protein condensates in phase separation from nano-scale to micro-scale in solution and living cells, it is difficult for the fluorescence imaging method and conventional FCS to fully reflect the real state of protein phase separation in the solution due to the low spatio-temporal resolution of the conventional fluorescence imaging method and the limited detection area of FCS. Here, we proposed a novel method for studying the protein phase separation process by objective scanning-based fluorescence cross-correlation spectroscopy (Scan-FCCS). In this study, CRDBP proteins were used as a model and respectively fused with fluorescent proteins (EGFP and mCherry). We first compared conventional FCS and Scan-FCS methods for characterizing the CRDBP protein phase separation behaviors and found that the reproducibility of Scan-FCS is significantly improved by the scanning mode. We studied the self-fusion process of mCherry-CRDBP and EGFP-CRDBP and observed that the phase change concentration of CRDBP was 25 nM and the fusion of mCherry-CRDBP and EGFP-CRDBP at 500 nM was completed within 70 min. We studied the effects of salt concentration and molecular crowding agents on the phase separation of CRDBP and found that salt can prevent the self-fusion of CRDBP and molecular crowding agents can improve the self-fusion of CRDBP. Furthermore, we found the recruitment behavior of CRDBP to β-catenin proteins and studied their recruitment dynamics. Compared to conventional FCS, Scan-FCCS can significantly improve the reproducibility of measurements due to the dramatic increase of detection zone, and more importantly, this method can provide information about self-fusion and recruitment dynamics in protein phase separation.
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Affiliation(s)
- Jian Liu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Wenxin Yu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiangyi Huang
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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Bagheri Y, Ali AA, You M. Current Methods for Detecting Cell Membrane Transient Interactions. Front Chem 2020; 8:603259. [PMID: 33365301 PMCID: PMC7750205 DOI: 10.3389/fchem.2020.603259] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Short-lived cell membrane complexes play a key role in regulating cell signaling and communication. Many of these complexes are formed based on low-affinity and transient interactions among various lipids and proteins. New techniques have emerged to study these previously overlooked membrane transient interactions. Exciting functions of these transient interactions have been discovered in cellular events such as immune signaling, host-pathogen interactions, and diseases such as cancer. In this review, we have summarized current experimental methods that allow us to detect and analyze short-lived cell membrane protein-protein, lipid-protein, and lipid-lipid interactions. These methods can provide useful information about the strengths, kinetics, and/or spatial patterns of membrane transient interactions. However, each method also has its own limitations. We hope this review can be used as a guideline to help the audience to choose proper approaches for studying membrane transient interactions in different membrane trafficking and cell signaling events.
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Affiliation(s)
| | | | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
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Ng XW, Sampath K, Wohland T. Fluorescence Correlation and Cross-Correlation Spectroscopy in Zebrafish. Methods Mol Biol 2019; 1863:67-105. [PMID: 30324593 DOI: 10.1007/978-1-4939-8772-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
There has been increasing interest in biophysical studies on live organisms to gain better insights into physiologically relevant biological events at the molecular level. Zebrafish (Danio rerio) is a viable vertebrate model to study such events due to its genetic and evolutionary similarities to humans, amenability to less invasive fluorescence techniques owing to its transparency and well-characterized genetic manipulation techniques. Fluorescence techniques used to probe biomolecular dynamics and interactions of molecules in live zebrafish embryos are therefore highly sought-after to bridge molecular and developmental events. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are two robust techniques that provide molecular level information on dynamics and interactions respectively. Here, we detail the steps for applying confocal FCS and FCCS, in particular single-wavelength FCCS (SW-FCCS), in live zebrafish embryos, beginning with sample preparation, instrumentation, calibration, and measurements on the FCS/FCCS instrument and ending with data analysis.
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Affiliation(s)
- Xue Wen Ng
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Thorsten Wohland
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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Spectral and structural analysis of large Stokes shift fluorescent protein dKeima570. J Microbiol 2018; 56:822-827. [DOI: 10.1007/s12275-018-8319-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 02/05/2023]
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Mücke N, Kämmerer L, Winheim S, Kirmse R, Krieger J, Mildenberger M, Baßler J, Hurt E, Goldmann WH, Aebi U, Toth K, Langowski J, Herrmann H. Assembly Kinetics of Vimentin Tetramers to Unit-Length Filaments: A Stopped-Flow Study. Biophys J 2018; 114:2408-2418. [PMID: 29754715 DOI: 10.1016/j.bpj.2018.04.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/20/2018] [Accepted: 04/19/2018] [Indexed: 01/01/2023] Open
Abstract
Intermediate filaments (IFs) are principal components of the cytoskeleton, a dynamic integrated system of structural proteins that provides the functional architecture of metazoan cells. They are major contributors to the elasticity of cells and tissues due to their high mechanical stability and intrinsic flexibility. The basic building block for the assembly of IFs is a rod-like, 60-nm-long tetrameric complex made from two antiparallel, half-staggered coiled coils. In low ionic strength, tetramers form stable complexes that rapidly assemble into filaments upon raising the ionic strength. The first assembly products, "frozen" by instantaneous chemical fixation and viewed by electron microscopy, are 60-nm-long "unit-length" filaments (ULFs) that apparently form by lateral in-register association of tetramers. ULFs are the active elements of IF growth, undergoing longitudinal end-to-end annealing with one another and with growing filaments. Originally, we have employed quantitative time-lapse atomic force and electron microscopy to analyze the kinetics of vimentin-filament assembly starting from a few seconds to several hours. To obtain detailed quantitative insight into the productive reactions that drive ULF formation, we now introduce a "stopped-flow" approach in combination with static light-scattering measurements. Thereby, we determine the basic rate constants for lateral assembly of tetramers to ULFs. Processing of the recorded data by a global fitting procedure enables us to describe the hierarchical steps of IF formation. Specifically, we propose that tetramers are consumed within milliseconds to yield octamers that are obligatory intermediates toward ULF formation. Although the interaction of tetramers is diffusion controlled, it is strongly driven by their geometry to mediate effective subunit targeting. Importantly, our model conclusively reflects the previously described occurrence of polymorphic ULF and mature filaments in terms of their number of tetramers per cross section.
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Affiliation(s)
- Norbert Mücke
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Lara Kämmerer
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Stefan Winheim
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Robert Kirmse
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jan Krieger
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Maria Mildenberger
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jochen Baßler
- Biochemistry Center of Heidelberg University, Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, Heidelberg, Germany
| | - Wolfgang H Goldmann
- Department of Physics, Biophysics group, Friedrich-Alexander-University of Erlangen-Nuremberg, Erlangen, Germany
| | - Ueli Aebi
- Biozentrum, University of Basel, Basel, Switzerland
| | - Katalin Toth
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Harald Herrmann
- Institute of Neuropathology, University Hospital Erlangen, Erlangen, Germany; Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany.
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Wang L, Xue Y, Xing J, Song K, Lin J. Exploring the Spatiotemporal Organization of Membrane Proteins in Living Plant Cells. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:525-551. [PMID: 29489393 DOI: 10.1146/annurev-arplant-042817-040233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plasma membrane proteins have important roles in transport and signal transduction. Deciphering the spatiotemporal organization of these proteins provides crucial information for elucidating the links between the behaviors of different molecules. However, monitoring membrane proteins without disrupting their membrane environment remains difficult. Over the past decade, many studies have developed single-molecule techniques, opening avenues for probing the stoichiometry and interactions of membrane proteins in their native environment by providing nanometer-scale spatial information and nanosecond-scale temporal information. In this review, we assess recent progress in the development of labeling and imaging technology for membrane protein analysis. We focus in particular on several single-molecule techniques for quantifying the dynamics and assembly of membrane proteins. Finally, we provide examples of how these new techniques are advancing our understanding of the complex biological functions of membrane proteins.
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Affiliation(s)
- Li Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Yiqun Xue
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jingjing Xing
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Kai Song
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China;
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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Detecting ligand interactions in real time on living bacterial cells. Appl Microbiol Biotechnol 2018; 102:4193-4201. [PMID: 29550990 PMCID: PMC5895670 DOI: 10.1007/s00253-018-8919-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 11/04/2022]
Abstract
Time-resolved analysis assays of receptor-ligand interactions are fundamental in basic research and drug discovery. Adequate methods are well developed for the analysis of recombinant proteins such as antibody-antigen interactions. However, assays for time-resolved ligand-binding processes on living cells are still rare, in particular within microbiology. In this report, the real-time cell-binding assay (RT-CBA) technology LigandTracer®, originally designed for mammalian cell culture, was extended to cover Gram-positive and Gram-negative bacteria. This required the development of new immobilization methods for bacteria, since LigandTracer depends on cells being firmly attached to a Petri dish. The evaluated Escherichia coli CJ236 and BL21 as well as Staphylococcus carnosus TM300 strains were immobilized to plastic Petri dishes using antibody capture, allowing us to depict kinetic binding traces of fluorescently labeled antibodies directed against surface-displayed bacterial proteins for as long as 10–15 h. Interaction parameters, such as the affinity and kinetic constants, could be estimated with high precision (coefficient of variation 9–44%) and the bacteria stayed viable for at least 16 h. The other tested attachment protocols were inferior to the antibody capture approach. Our attachment protocol is generic and could potentially also be applied to other assays and purposes.
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Krüger D, Ebenhan J, Werner S, Bacia K. Measuring Protein Binding to Lipid Vesicles by Fluorescence Cross-Correlation Spectroscopy. Biophys J 2017; 113:1311-1320. [PMID: 28697897 DOI: 10.1016/j.bpj.2017.06.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/21/2017] [Accepted: 06/08/2017] [Indexed: 11/26/2022] Open
Abstract
Fluorescence correlation spectroscopy has been previously used to investigate peptide and protein binding to lipid membranes, as it allows for very low amounts of sample, short measurement times and equilibrium binding conditions. Labeling only one of the binding partners, however, comes with certain drawbacks, as it relies on identifying binding events by a change in diffusion coefficient. Since peptide and protein aggregation can obscure specific binding, and since non-stoichiometric binding necessitates the explicit choice of a statistical distribution for the number of bound ligands, we additionally label the liposomes and perform dual-color fluorescence cross-correlation spectroscopy (dcFCCS). We develop a theoretical framework showing that dcFCCS amplitudes allow calculation of the degree of ligand binding and the concentration of unbound ligand, leading to a model-independent binding curve. As the degree of labeling of the ligands does not factor into the measured quantities, it is permissible to mix labeled and unlabeled ligand, thereby extending the range of usable protein concentrations and accessible dissociation constants, KD. The total protein concentration, but not the fraction of labeled protein, needs to be known. In this work, we apply our dcFCCS analysis scheme to Sar1p, a protein of the COPII complex, which binds "major-minor-mix" liposomes. A Langmuir isotherm model yields KD=(2.1±1.1)μM as the single-site dissociation constant. The dcFCCS framework presented here is highly versatile for biophysical analysis of binding interactions. It may be applied to many types of fluorescently labeled ligands and small diffusing particles, including nanodiscs and liposomes containing membrane protein receptors.
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Affiliation(s)
- Daniela Krüger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Ebenhan
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Stefan Werner
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Kirsten Bacia
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
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9
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Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc 2015; 3:042003. [DOI: 10.1088/2050-6120/3/4/042003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Abstract
Systems biology has recently achieved significant success in the understanding of complex interconnected phenomena such as cell polarity and migration. In this context, the definition of systems biology has come to encompass the integration of quantitative measurements with sophisticated modeling approaches. This article will review recent progress in live cell imaging technologies that have expanded the possibilities of quantitative in vivo measurements, particularly in regards to molecule counting and quantitative measurements of protein concentration and dynamics. These methods have gained and continue to gain popularity with the biological community. In general, we will discuss three broad categories: protein interactions, protein quantitation, and protein dynamics.
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Affiliation(s)
- Sarah E Smith
- a Stowers Institute for Medical Research ; Kansas City , MO USA
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