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Li JY, Zhou CM, Jin RL, Song JH, Yang KC, Li SL, Tan BH, Li YC. The detection methods currently available for protein aggregation in neurological diseases. J Chem Neuroanat 2024; 138:102420. [PMID: 38626816 DOI: 10.1016/j.jchemneu.2024.102420] [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: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.
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Affiliation(s)
- Jing-Yi Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Cheng-Mei Zhou
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Rui-Lin Jin
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Jia-Hui Song
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Ke-Chao Yang
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Shu-Lei Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Bai-Hong Tan
- Laboratory Teaching Center of Basic Medicine, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Yan-Chao Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China.
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Fujioka H, Murao Y, Okinaka M, John Spratt S, Shou J, Kawatani M, Kojima R, Tachibana R, Urano Y, Ozeki Y, Kamiya M. Cyano-Hydrol green derivatives: Expanding the 9-cyanopyronin-based resonance Raman vibrational palette. Bioorg Med Chem Lett 2024; 106:129757. [PMID: 38636718 DOI: 10.1016/j.bmcl.2024.129757] [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: 02/21/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
9-cyanopyronin is a promising scaffold that exploits resonance Raman enhancement to enable sensitive, highly multiplexed biological imaging. Here, we developed cyano-Hydrol Green (CN-HG) derivatives as resonance Raman scaffolds to expand the color palette of 9-cyanopyronins. CN-HG derivatives exhibit sufficiently long wavelength absorption to produce strong resonance Raman enhancement for near-infrared (NIR) excitation, and their nitrile peaks are shifted to a lower frequency than those of 9-cyanopyronins. The fluorescence of CN-HG derivatives is strongly quenched due to the lack of the 10th atom, unlike pyronin derivatives, and this enabled us to detect spontaneous Raman spectra with high signal-to-noise ratios. CN-HG derivatives are powerful candidates for high performance vibrational imaging.
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Affiliation(s)
- Hiroyoshi Fujioka
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yuta Murao
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Momoko Okinaka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Spencer John Spratt
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Jingwen Shou
- Department of Electrical Engineering and Information Systems, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Minoru Kawatani
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Tachibana
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuyuki Ozeki
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan; Department of Electrical Engineering and Information Systems, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mako Kamiya
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan; Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Research Center for Autonomous Systems Meterialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho. Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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Brøndsted F, Stains CI. Heteroatom-Substituted Xanthene Fluorophores Enter the Shortwave-Infrared Region. Photochem Photobiol 2022; 98:400-403. [PMID: 34953073 PMCID: PMC8930474 DOI: 10.1111/php.13578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022]
Abstract
This article is a highlight of the paper by Ivanic and Schnermann et al. in this issue of Photochemistry and Photobiology (Daly et al. Photochem. Photobiol. 2022). The collaborative team utilized computational approaches to investigate the influence of electron-withdrawing groups at the 10' position of tetramethylrhodamine (TMR). Leveraging this information, the team was able to extend the emission of the TMR scaffold into the shortwave-infrared region (SWIR, 1000-2500 nm) by incorporation of a ketone functional group at the 10' position (Daly et al. Photochem. Photobiol. 2022). This work provides the first example of a TMR derivative with peak SWIR emission (λabs : 862 nm, λem : 1058 nm). The authors utilize the ketone rhodamine scaffold to generate fluorogenic, pH-responsive reporters. This work demonstrates the potential of the classic xanthene scaffold for use as a SWIR reporter, an important step in the ultimate expansion of the repertoire of small-molecule organic fluorophore scaffolds available for deep-tissue imaging applications.
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Affiliation(s)
- Frederik Brøndsted
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Cliff I. Stains
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA,University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, USA,Corresponding author: (Cliff I. Stains)
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Michler's hydrol blue elucidates structural differences in prion strains. Proc Natl Acad Sci U S A 2020; 117:29677-29683. [PMID: 33168711 DOI: 10.1073/pnas.2001732117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Yeast prions provide self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Classic dyes, such as thioflavin T and Congo red, exhibit large increases in fluorescence when bound to amyloids, but these dyes are not sensitive to local structural differences that distinguish amyloid strains. Here we describe the use of Michler's hydrol blue (MHB) to investigate fibrils formed by the weak and strong prion fibrils of Sup35NM and find that MHB differentiates between these two polymorphs. Quantum mechanical time-dependent density functional theory (TDDFT) calculations indicate that the fluorescence properties of amyloid-bound MHB can be correlated to the change of binding site polarity and that a tyrosine to phenylalanine substitution at a binding site could be detected. Through the use of site-specific mutants, we demonstrate that MHB is a site-specific environmentally sensitive probe that can provide structural details about amyloid fibrils and their polymorphs.
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Lin CY, Romei MG, Oltrogge LM, Mathews II, Boxer SG. Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins. J Am Chem Soc 2019; 141:15250-15265. [PMID: 31450887 DOI: 10.1021/jacs.9b07152] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Matthew G Romei
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Luke M Oltrogge
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road , Menlo Park , California 94025 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305 , United States
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Franke JM, Raliski BK, Boggess SC, Natesan DV, Koretsky ET, Zhang P, Kulkarni RU, Deal PE, Miller EW. BODIPY Fluorophores for Membrane Potential Imaging. J Am Chem Soc 2019; 141:12824-12831. [PMID: 31339313 DOI: 10.1021/jacs.9b05912] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorophores based on the BODIPY scaffold are prized for their tunable excitation and emission profiles, mild syntheses, and biological compatibility. Improving the water-solubility of BODIPY dyes remains an outstanding challenge. The development of water-soluble BODIPY dyes usually involves direct modification of the BODIPY fluorophore core with ionizable groups or substitution at the boron center. While these strategies are effective for the generation of water-soluble fluorophores, they are challenging to implement when developing BODIPY-based indicators: direct modification of BODIPY core can disrupt the electronics of the dye, complicating the design of functional indicators; and substitution at the boron center often renders the resultant BODIPY incompatible with the chemical transformations required to generate fluorescent sensors. In this study, we show that BODIPYs bearing a sulfonated aromatic group at the meso position provide a general solution for water-soluble BODIPYs. We outline the route to a suite of 5 new sulfonated BODIPYs with 2,6-disubstitution patterns spanning a range of electron-donating and -withdrawing propensities. To highlight the utility of these new, sulfonated BODIPYs, we further functionalize them to access 13 new, BODIPY-based, voltage-sensitive fluorophores (VF). The most sensitive of these BODIPY VF dyes displays a 48% ΔF/F per 100 mV in mammalian cells. Two additional BODIPY VFs show good voltage sensitivity (≥24% ΔF/F) and excellent brightness in cells. These compounds can report on action potential dynamics in both mammalian neurons and human stem cell-derived cardiomyocytes. Accessing a range of substituents in the context of a water-soluble BODIPY fluorophore provides opportunities to tune the electronic properties of water-soluble BODIPY dyes for functional indicators.
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Yang C, Zhang J, Peng WT, Sheng W, Liu D, Kuttipillai PS, Young M, Donahue MR, Levine BG, Borhan B, Lunt RR. Impact of Stokes Shift on the Performance of Near-Infrared Harvesting Transparent Luminescent Solar Concentrators. Sci Rep 2018; 8:16359. [PMID: 30397272 PMCID: PMC6218549 DOI: 10.1038/s41598-018-34442-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022] Open
Abstract
Visibly transparent luminescent solar concentrators (TLSC) have the potential to turn existing infrastructures into net-zero-energy buildings. However, the reabsorption loss currently limits the device performance and scalability. This loss is typically defined by the Stokes shift between the absorption and emission spectra of luminophores. In this work, the Stokes shifts (SS) of near-infrared selective-harvesting cyanines are altered by substitution of the central methine carbon with dialkylamines. We demonstrate varying SS with values over 80 nm and ideal infrared-visible absorption cutoffs. The corresponding TLSC with such modification shows a power conversion efficiency (PCE) of 0.4% for a >25 cm2 device area with excellent visible transparency >80% and up to 0.6% PCE over smaller areas. However, experiments and simulations show that it is not the Stokes shift that is critical, but the total degree of overlap that depends on the shape of the absorption tails. We show with a series of SS-modulated cyanine dyes that the SS is not necessarily correlated to improvements in performance or scalability. Accordingly, we define a new parameter, the overlap integral, to sensitively correlate reabsorption losses in any LSC. In deriving this parameter, new approaches to improve the scalability and performance are discussed to fully optimize TLSC designs to enhance commercialization efforts.
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Affiliation(s)
- Chenchen Yang
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Jun Zhang
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Wei-Tao Peng
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Wei Sheng
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Dianyi Liu
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Padmanaban S Kuttipillai
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Margaret Young
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Matthew R Donahue
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Benjamin G Levine
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Richard R Lunt
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Physics and Astronomy, Michigan State University, East Lansing, MI, 48824, USA.
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8
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Novel benzophenone-3 derivatives with promising potential as UV filters: Relationship between structure, photoprotective potential and phototoxicity. Eur J Pharm Sci 2017; 101:200-210. [DOI: 10.1016/j.ejps.2017.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 01/26/2023]
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Abstract
Theories of color in cyanine dyes have evolved around the idea of a "resonance" of structures with distinct bonding and charge localization. Understanding the emergence of resonance models from the underlying many-electron problem remains a central issue for these systems. Here, the issue is addressed using a maximum-entropy approach to valence-bond representations of state-averaged complete-active space self-consistent field models. The approach allows calculation of energies and couplings of high-energy valence-bond structures that mediate superexchange couplings and chemical bonding. A series of valence-bond Hamiltonians for a series of bridge-substituted derivatives of Michler's hydrol blue (a monomethine cyanine) is presented. The Hamiltonians are approximated with a simple linear model parametrized by the Brown-Okamoto σp+ parameter of the bridge substituent. A quantitative lower bound on σp+, beyond which a resonant cyanine-like ground state will not exist, is presented. The large effective coupling in two-state resonance models emerges from superexchange associated with either covalent bonding or charge-carrier delocalization, with the former contribution significantly the stronger. The results provide ab initio justification for empirical diabatic-state models of methine optical response. They are of general interest for understanding the optoelectronic response in cyanines.
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Affiliation(s)
- Seth Olsen
- School of Mathematics and Physics, The University of Queensland , Brisbane QLD 4072, Australia
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Olsen S. Canonical-ensemble state-averaged complete active space self-consistent field (SA-CASSCF) strategy for problems with more diabatic than adiabatic states: Charge-bond resonance in monomethine cyanines. J Chem Phys 2015; 142:044116. [DOI: 10.1063/1.4904298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Misra R, Maity D, Bhattacharyya S. Deciphering the role of multiple hydrogen bonding sites on the microsolvation of 3-(phenylamino)-2-cyclohexen-1-one with water in the excited states. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Olsen S. Why Bindschedler’s Green Is Redder Than Michler’s Hydrol Blue. J Phys Chem A 2013; 117:2455-68. [DOI: 10.1021/jp309006e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seth Olsen
- School of Mathematics
and Physics, The University of Queensland, Brisbane
QLD 4072 Australia
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Olsen S, McKenzie RH. A three-state effective Hamiltonian for symmetric cationic diarylmethanes. J Chem Phys 2012; 136:234313. [PMID: 22779599 DOI: 10.1063/1.4728158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We analyze the low-energy electronic structure of a series of symmetric cationic diarylmethanes, which are bridge-substituted derivatives of Michler's Hydrol Blue. We use a four-electron, three-orbital complete active space self-consistent field and multi-state multi-reference perturbation theory model to calculate a three-state diabatic effective Hamiltonian for each dye in the series. We exploit an isolobal analogy between the active spaces of the self-consistent field solutions for each dye to represent the electronic structure in a set of analogous diabatic states. The diabatic states can be identified with the bonding structures in classical resonance-theoretic models of cyanine dyes. We identify diabatic states with opposing charge and bond-order localization, analogous to the classical resonance structures, and a third state with charge on the bridge. While the left- and right-charged structures are similar for all dyes, the structure of the bridge-charged diabatic state, and the Hamiltonian matrix elements connected to it, change significantly across the series. The change is correlated with an inversion of the sign of the charge carrier on the bridge, which changes from an electron pair to a hole as the series is traversed.
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Affiliation(s)
- Seth Olsen
- School of Mathematics and Physics, The University of Queensland, Brisbane, QLD 4072, Australia.
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Olsen S, McKenzie RH. A two-state model of twisted intramolecular charge-transfer in monomethine dyes. J Chem Phys 2012; 137:164319. [DOI: 10.1063/1.4762561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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