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Wüstner D. Dynamic Mode Decomposition of Fluorescence Loss in Photobleaching Microscopy Data for Model-Free Analysis of Protein Transport and Aggregation in Living Cells. SENSORS (BASEL, SWITZERLAND) 2022; 22:4731. [PMID: 35808232 PMCID: PMC9269098 DOI: 10.3390/s22134731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 02/05/2023]
Abstract
The phase separation and aggregation of proteins are hallmarks of many neurodegenerative diseases. These processes can be studied in living cells using fluorescent protein constructs and quantitative live-cell imaging techniques, such as fluorescence recovery after photobleaching (FRAP) or the related fluorescence loss in photobleaching (FLIP). While the acquisition of FLIP images is straightforward on most commercial confocal microscope systems, the analysis and computational modeling of such data is challenging. Here, a novel model-free method is presented, which resolves complex spatiotemporal fluorescence-loss kinetics based on dynamic-mode decomposition (DMD) of FLIP live-cell image sequences. It is shown that the DMD of synthetic and experimental FLIP image series (DMD-FLIP) allows for the unequivocal discrimination of subcellular compartments, such as nuclei, cytoplasm, and protein condensates based on their differing transport and therefore fluorescence loss kinetics. By decomposing fluorescence-loss kinetics into distinct dynamic modes, DMD-FLIP will enable researchers to study protein dynamics at each time scale individually. Furthermore, it is shown that DMD-FLIP is very efficient in denoising confocal time series data. Thus, DMD-FLIP is an easy-to-use method for the model-free detection of barriers to protein diffusion, of phase-separated protein assemblies, and of insoluble protein aggregates. It should, therefore, find wide application in the analysis of protein transport and aggregation, in particular in relation to neurodegenerative diseases and the formation of protein condensates in living cells.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology and Physics of Life Sciences (PhyLife) Center, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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2
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Jain P, Motosuke M. Fluorescence Anisotropy Studies on Bodipy (Pyrromethene 546) Dye as a Novel Thermal Probe. J Fluoresc 2022; 32:737-743. [DOI: 10.1007/s10895-021-02868-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 12/17/2022]
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Liu YX, Xie TJ, Li CH, Ye QC, Tian LL, Li YF, Huang CZ, Zhen SJ. A crosslinked submicro-hydrogel formed by DNA circuit-driven protein aggregation amplified fluorescence anisotropy for biomolecules detection. Anal Chim Acta 2021; 1154:338319. [PMID: 33736800 DOI: 10.1016/j.aca.2021.338319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 11/25/2022]
Abstract
Protein is an excellent molecular mass amplifier without fluorescence quenching effect for fluorescence anisotropy (FA) assay. However, in traditional protein amplified FA methods, the binding ratio between amplifier and dye-modified probe is 1:1 or one target can only induce FA change of one fluorophore on probe, resulting in low sensitivity. Herein, we developed a simple FA strategy with high accuracy and sensitivity by using a crosslinked submicro-hydrogel that was formed through a catalyzed hairpin assembly (CHA) assisted protein aggregation as a novel FA amplifier. In the presence of catalyst, the CHA process was initiated through the toehold-mediated strand exchange reaction, which led to the formation of a dye and biotin-labeled Y-shaped H1-H2 duplex (YHD) and recycling of catalyst. With the introduction of streptavidin, a crosslinked submicro-hydrogel was formed by strong binding affinity between biotin on YHD and streptavidin, resulting in an increased FA of fluorescent dye. After rational design of the catalyst sequence, this method has been utilized for the detection of miRNA-145, staphylococcal enterotoxin B (SEB) and ATP with an LOD of 2.5 nM, 92 pg mL-1 and 3.6 μM, respectively. Moreover, this FA assay has been successfully applied for direct detection of target in biological samples, demonstrating its practicality in complex biological systems.
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Affiliation(s)
- Yu Xin Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715, Chongqing, PR China
| | - Tian Jin Xie
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715, Chongqing, PR China
| | - Chun Hong Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, 400715, Chongqing, PR China
| | - Qi Chao Ye
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715, Chongqing, PR China
| | - Li Li Tian
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715, Chongqing, PR China
| | - Yuan Fang Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715, Chongqing, PR China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, 400715, Chongqing, PR China
| | - Shu Jun Zhen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, 400715, Chongqing, PR China.
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4
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Fluorescence-based techniques for the detection of the oligomeric status of proteins: implication in amyloidogenic diseases. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:671-685. [PMID: 33564930 DOI: 10.1007/s00249-021-01505-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/10/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Intrinsically disordered proteins (IDPs) have captured attention in the last couple of decades due to their functional roles despite a lack of specific structure. Moreover, these proteins are found to be highly aggregation prone depending on the mutational and environmental changes to which they are subjected. The aggregation of such proteins either in the intracellular context or extracellular matrix is associated with several adverse pathophysiological conditions such as Alzheimer's, Parkinson's, and Huntington's diseases, Spinocerebellar ataxia, and Type-II diabetes. Interestingly, it has been noted that the smaller oligomers formed by IDPs are more toxic to cells than their larger aggregates. This necessitates the development of techniques that can detect the smaller oligomers formed by IDPs for diagnosis of such diseases during their early onset. Fluorescence-based spectroscopic and microscopic techniques are highly effective as compared to other techniques for the evaluation of protein oligomerization, organization, and dynamics. In this review, we discuss several fluorescence-based techniques including fluorescence/Förster resonance energy transfer (FRET), homo-FRET, fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), fluorescence lifetime imaging (FLIM), and photobleaching image correlation spectroscopy (pbICS) that are routinely used to identify protein oligomers in extracellular and intracellular matrices.
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Fluorescence Anisotropy Sensor Comprising a Dual Hollow-Core Antiresonant Fiber Polarization Beam Splitter. SENSORS 2020; 20:s20113321. [PMID: 32545205 PMCID: PMC7308924 DOI: 10.3390/s20113321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/23/2022]
Abstract
Fluorescence anisotropy imaging and sensing is a widely recognized method for studying molecular orientation and mobility. However, introducing this technique to in vivo systems is a challenging task, especially when one considers multiphoton excitation methods. Past two decades have brought a possible solution to this issue in the form of hollow-core antiresonant fibers (HC-ARFs). The continuous development of their fabrication technology has resulted in the appearance of more and more sophisticated structures. One of the most promising concepts concerns dual hollow-core antiresonant fibers (DHC-ARFs), which can be used to split and combine optical signals, effectively working as optical fiber couplers. In this paper, the design of a fluorescence anisotropy sensor based on a DHC-ARF structure is presented. The main purpose of the proposed DHC-ARF is multiphoton-excited fluorescence spectroscopy; however, other applications are also possible.
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Hansen CV, Schroll HJ, Wüstner D. A discontinuous Galerkin model for fluorescence loss in photobleaching of intracellular polyglutamine protein aggregates. BMC BIOPHYSICS 2018; 11:7. [PMID: 30519460 PMCID: PMC6264036 DOI: 10.1186/s13628-018-0046-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 10/30/2018] [Indexed: 12/03/2022]
Abstract
Background Intracellular phase separation and aggregation of proteins with extended poly-glutamine (polyQ) stretches are hallmarks of various age-associated neurodegenerative diseases. Progress in our understanding of such processes heavily relies on quantitative fluorescence imaging of suitably tagged proteins. Fluorescence loss in photobleaching (FLIP) is particularly well-suited to study the dynamics of protein aggregation in cellular models of Chorea Huntington and other polyQ diseases, as FLIP gives access to the full spatio-temporal profile of intensity changes in the cell geometry. In contrast to other methods, also dim aggregates become visible during time evolution of fluorescence loss in cellular compartments. However, methods for computational analysis of FLIP data are sparse, and transport models for estimation of transport and diffusion parameters from experimental FLIP sequences are missing. Results In this paper, we present a computational method for analysis of FLIP imaging experiments of intracellular polyglutamine protein aggregates also called inclusion bodies (IBs). By this method, we can determine the diffusion constant and nuclear membrane transport coefficients of polyQ proteins as well as the exchange rates between aggregates and the cytoplasm. Our method is based on a reaction-diffusion multi-compartment model defined on a mesh obtained by segmentation of the cell images from the FLIP sequence. The discontinuous Galerkin (DG) method is used for numerical implementation of our model in FEniCS, which greatly reduces the computing time. The method is applied to representative experimental FLIP sequences, and consistent estimates of all transport parameters are obtained. Conclusions By directly estimating the transport parameters from live-cell image sequences using our new computational FLIP approach surprisingly fast exchange dynamics of mutant Huntingtin between cytoplasm and dim IBs could be revealed. This is likely relevant also for other polyQ diseases. Thus, our method allows for quantifying protein dynamics at different stages of the protein aggregation process in cellular models of neurodegeneration. Electronic supplementary material The online version of this article (10.1186/s13628-018-0046-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christian V Hansen
- 1Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, Odense M, 5230 Denmark
| | - Hans J Schroll
- 1Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, Odense M, 5230 Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, Campusvej 55, Odense M, 5230 Denmark
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Zhao TT, Peng ZW, Yuan D, Zhen SJ, Huang CZ, Li YF. Metal-organic gel enhanced fluorescence anisotropy for sensitive detection of prostate specific antigen. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 192:328-332. [PMID: 29174667 DOI: 10.1016/j.saa.2017.10.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/13/2017] [Accepted: 10/27/2017] [Indexed: 05/27/2023]
Abstract
In this contribution, we demonstrated that Cu-based metal-organic gel (Cu-MOG) was able to serve as a novel amplification platform for fluorescence anisotropy (FA) assay for the first time, which was confirmed by the sensitive detection of a common cancer biomarker, prostate specific antigen (PSA). The dye-labeled probe aptamer (PA) product was adsorbed onto the benzimidazole derivative-containing Cu-MOG via electrostatic incorporation and strong π-π stacking interactions, which significantly increased the FA value due to the enlargement of the molecular volume of the PA/Cu-MOG complex. With the introduction of target PSA, the FA value was obviously decreased on account of the specific recognition between PSA and PA which resulted in the detachment of PA from the surface of MOG. The linear range was from 0.5-8ng/mL, with a detection limit of 0.33ng/mL. Our work has thus helped to demonstrate promising application of MOG material in the fields of biomolecules analysis and disease diagnosis.
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Affiliation(s)
- Ting Ting Zhao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Zhe Wei Peng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Dan Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yuan Fang Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
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8
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Halfmann R. A glass menagerie of low complexity sequences. Curr Opin Struct Biol 2016; 38:18-25. [PMID: 27258703 DOI: 10.1016/j.sbi.2016.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/06/2016] [Accepted: 05/11/2016] [Indexed: 10/24/2022]
Abstract
Remarkably simple proteins play outsize roles in the execution of developmental complexity within biological systems. Sequence information determines structure and hence function, so how do low complexity sequences fulfill their functions? Recent discoveries are raising the curtain on a new dimension of the sequence-structure paradigm. In it, function derives not from the structures of individual proteins, but instead, from dynamic material properties of entire ensembles of the proteins acting in unison through phase changes. These phases include liquids, one-dimensional crystals, and - as elaborated herein - even glasses. The peculiar thermodynamics of glass-like protein assemblies, in particular, illuminate new principles of information flow through and, at times, orthogonal to the central dogma of molecular biology.
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Affiliation(s)
- Randal Halfmann
- Stowers Institute for Medical Research, 1000 E. 50th St., Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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9
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Darrow MC, Sergeeva OA, Isas JM, Galaz-Montoya JG, King JA, Langen R, Schmid MF, Chiu W. Structural Mechanisms of Mutant Huntingtin Aggregation Suppression by the Synthetic Chaperonin-like CCT5 Complex Explained by Cryoelectron Tomography. J Biol Chem 2015; 290:17451-61. [PMID: 25995452 DOI: 10.1074/jbc.m115.655373] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 11/06/2022] Open
Abstract
Huntington disease, a neurodegenerative disorder characterized by functional deficits and loss of striatal neurons, is linked to an expanded and unstable CAG trinucleotide repeat in the huntingtin gene (HTT). This DNA sequence translates to a polyglutamine repeat in the protein product, leading to mutant huntingtin (mHTT) protein aggregation. The aggregation of mHTT is inhibited in vitro and in vivo by the TCP-1 ring complex (TRiC) chaperonin. Recently, a novel complex comprised of a single type of TRiC subunit has been reported to inhibit mHTT aggregation. Specifically, the purified CCT5 homo-oligomer complex, when compared with TRiC, has a similar structure, ATP use, and substrate refolding activity, and, importantly, it also inhibits mHTT aggregation. Using an aggregation suppression assay and cryoelectron tomography coupled with a novel computational classification method, we uncover the interactions between the synthetic CCT5 complex (∼ 1 MDa) and aggregates of mutant huntingtin exon 1 containing 46 glutamines (mHTTQ46-Ex1). We find that, in a similar fashion to TRiC, synthetic CCT5 complex caps mHTT fibrils at their tips and encapsulates mHTT oligomers, providing a structural description of the inhibition of mHTTQ46-Ex1 by CCT5 complex and a shared mechanism of mHTT inhibition between TRiC chaperonin and the CCT5 complex: cap and contain.
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Affiliation(s)
- Michele C Darrow
- From the National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Oksana A Sergeeva
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Jose M Isas
- the Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Jesús G Galaz-Montoya
- From the National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Jonathan A King
- the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and
| | - Ralf Langen
- the Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Michael F Schmid
- From the National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Wah Chiu
- From the National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030,
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10
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Xiao X, Li YF, Huang CZ, Zhen SJ. A novel graphene oxide amplified fluorescence anisotropy assay with improved accuracy and sensitivity. Chem Commun (Camb) 2015; 51:16080-3. [DOI: 10.1039/c5cc05902j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel and versatile graphene oxide (GO) amplified fluorescence anisotropy (FA) strategy with improved accuracy and sensitivity has been successfully developed.
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Affiliation(s)
- Xue Xiao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing
| | - Yuan Fang Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing
| | - Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing
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