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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.
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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
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2
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Hilt S, Liu R, Maezawa I, Rojalin T, Aung HH, Budamagunta M, Slez R, Gong Q, Carney RP, Voss JC. Novel Stilbene-Nitroxyl Hybrid Compounds Display Discrete Modulation of Amyloid Beta Toxicity and Structure. Front Chem 2022; 10:896386. [PMID: 35720993 PMCID: PMC9204515 DOI: 10.3389/fchem.2022.896386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Several neurodegenerative diseases are driven by misfolded proteins that assemble into soluble aggregates. These "toxic oligomers" have been associated with a plethora of cellular dysfunction and dysregulation, however the structural features underlying their toxicity are poorly understood. A major impediment to answering this question relates to the heterogeneous nature of the oligomers, both in terms of structural disorder and oligomer size. This not only complicates elucidating the molecular etiology of these disorders, but also the druggability of these targets as well. We have synthesized a class of bifunctional stilbenes to modulate both the conformational toxicity within amyloid beta oligomers (AβO) and the oxidative stress elicited by AβO. Using a neuronal culture model, we demonstrate this bifunctional approach has the potential to counter the molecular pathogenesis of Alzheimer's disease in a powerful, synergistic manner. Examination of AβO structure by various biophysical tools shows that each stilbene candidate uniquely alters AβO conformation and toxicity, providing insight towards the future development of structural correctors for AβO. Correlations of AβO structural modulation and bioactivity displayed by each provides insights for future testing in vivo. The multi-target activity of these hybrid molecules represents a highly advantageous feature for disease modification in Alzheimer's, which displays a complex, multifactorial etiology. Importantly, these novel small molecules intervene with intraneuronal AβO, a necessary feature to counter the cycle of dysregulation, oxidative stress and inflammation triggered during the earliest stages of disease progression.
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Affiliation(s)
- Silvia Hilt
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Izumi Maezawa
- M.I.N.D. Institute and Department of Pathology and Laboratory Medicine, University of California, Davis, Davis, CA, United States
| | - Tatu Rojalin
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States
| | - Hnin H. Aung
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA, United States
- Research Division, California Air Resource Board, Sacramento, CA, United States
| | - Madhu Budamagunta
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Ryan Slez
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Randy P. Carney
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States
| | - John C. Voss
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Paramag Biosciences Inc., Davis, CA, United States
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3
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de Oliveira MAS, Hilt S, Chang CW, Lee C, Voss JC, Chan JW. Surface-enhanced Raman scattering sensing platform for detecting amyloid-β peptide interaction with an aggregation inhibitor. APPLIED OPTICS 2020; 59:7490-7495. [PMID: 32902446 DOI: 10.1364/ao.399307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
Soluble, small amyloid-β oligomers (AβO) are recognized as significant contributors to the pathology of Alzheimer's disease (AD). Although drugs for treating AD symptoms have been approved, no therapy targeting amyloid-β (Aβ) capable of modifying the course of the disease is available. In an effort to develop a label-free method for screening new anti-AD therapeutic agents, we show the use of a surface-enhanced Raman scattering (SERS) active substrate for detecting the interactions between Aβ peptides and spin-labeled fluorine (SLF), a peptide aggregation inhibitor. Changes in the peak positions and intensity ratios of two spectral peaks near 1600cm-1 and 2900cm-1 can be used to monitor the molecular interactions between SLF and Aβ. This study demonstrates the potential of SERS spectroscopy for rapidly screening and identifying new anti-Aβ therapeutic agents.
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How Fluorescent Tags Modify Oligomer Size Distributions of the Alzheimer Peptide. Biophys J 2018; 116:227-238. [PMID: 30638607 PMCID: PMC6350010 DOI: 10.1016/j.bpj.2018.12.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/14/2018] [Accepted: 12/03/2018] [Indexed: 11/30/2022] Open
Abstract
Within the complex aggregation process of amyloidogenic peptides into fibrils, early stages of aggregation play a central role and reveal fundamental properties of the underlying mechanism of aggregation. In particular, low-molecular-weight aggregates of the Alzheimer amyloid-β peptide (Aβ) have attracted increasing interest because of their role in cytotoxicity and neuronal apoptosis, typical of aggregation-related diseases. One of the main techniques used to characterize oligomeric stages is fluorescence spectroscopy. To this end, Aβ peptide chains are functionalized with fluorescent tags, often covalently bound to the disordered N-terminus region of the peptide, with the assumption that functionalization and presence of the fluorophore will not modify the process of self-assembly nor the final fibrillar structure. In this investigation, we systematically study the effects of four of the most commonly used fluorophores on the aggregation of Aβ (1–40). Time-resolved and single-molecule fluorescence spectroscopy have been chosen to monitor the oligomer populations at different fibrillation times, and transmission electron microscopy, atomic force microscopy and x-ray diffraction to investigate the structure of mature fibrils. Although the structures of the fibrils were only slightly affected by the fluorescent tags, the sizes of the detected oligomeric species varied significantly depending on the chosen fluorophore. In particular, we relate the presence of high-molecular-weight oligomers of Aβ (1–40) (as found for the fluorophores HiLyte 647 and Atto 655) to net-attractive, hydrophobic fluorophore-peptide interactions, which are weak in the case of HiLyte 488 and Atto 488. The latter leads for Aβ (1–40) to low-molecular-weight oligomers only, which is in contrast to Aβ (1–42). The disease-relevant peptide Aβ (1–42) displays high-molecular-weight oligomers even in the absence of significant attractive fluorophore-peptide interactions. Hence, our findings reveal the potentially high impact of the properties of fluorophores on transient aggregates, which needs to be included in the interpretation of experimental data of oligomers of fluorescently labeled peptides.
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A Bifunctional Anti-Amyloid Blocks Oxidative Stress and the Accumulation of Intraneuronal Amyloid-Beta. Molecules 2018; 23:molecules23082010. [PMID: 30103547 PMCID: PMC6222334 DOI: 10.3390/molecules23082010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/04/2018] [Accepted: 08/08/2018] [Indexed: 12/30/2022] Open
Abstract
There is growing recognition regarding the role of intracellular amyloid beta (Aβ) in the Alzheimer’s disease process, which has been linked with aberrant signaling and the disruption of protein degradation mechanisms. Most notably, intraneuronal Aβ likely underlies the oxidative stress and mitochondrial dysfunction that have been identified as key elements of disease progression. In this study, we employed fluorescence imaging to explore the ability of a bifunctional small molecule to reduce aggregates of intracellular Aβ and attenuate oxidative stress. Structurally, this small molecule is comprised of a nitroxide spin label linked to an amyloidophilic fluorene and is known as spin-labeled fluorene (SLF). The effect of the SLF on intracellular Aβ accumulation and oxidative stress was measured in MC65 cells, a human neuronal cell line with inducible expression of the amyloid precursor protein and in the N2a neuronal cell line treated with exogenous Aβ. Super-resolution microscopy imaging showed SLF decreases the accumulation of intracellular Aβ. Confocal microscopy imaging of MC65 cells treated with a reactive oxygen species (ROS)-sensitive dye demonstrated SLF significantly reduces the intracellular Aβ-induced ROS signal. In order to determine the contributions of the separate SLF moieties to these protective activities, experiments were also carried out on cells with nitroxides lacking the Aβ targeting domain or fluorene derivatives lacking the nitroxide functionality. The findings support a synergistic effect of SLF in counteracting both the conformational toxicity of both endogenous and exogenous Aβ, its promotion of ROS, and Aβ metabolism. Furthermore, these studies demonstrate an intimate link between ROS production and Aβ oligomer formation.
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Hilt S, Tang T, Walton JH, Budamagunta M, Maezawa I, Kálai T, Hideg K, Singh V, Wulff H, Gong Q, Jin LW, Louie A, Voss JC. A Metal-Free Method for Producing MRI Contrast at Amyloid-β. J Alzheimers Dis 2018; 55:1667-1681. [PMID: 27911291 DOI: 10.3233/jad-160279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Alzheimer's disease (AD) is characterized by depositions of the amyloid-β (Aβ) peptide in the brain. The disease process develops over decades, with substantial neurological loss occurring before a clinical diagnosis of dementia can be rendered. It is therefore imperative to develop methods that permit early detection and monitoring of disease progression. In addition, the multifactorial pathogenesis of AD has identified several potential avenues for AD intervention. Thus, evaluation of therapeutic candidates over lengthy trial periods also demands a practical, noninvasive method for measuring Aβ in the brain. Magnetic resonance imaging (MRI) is the obvious choice for such measurements, but contrast enhancement for Aβ has only been achieved using Gd(III)-based agents. There is great interest in gadolinium-free methods to image the brain. In this study, we provide the first demonstration that a nitroxide-based small-molecule produces MRI contrast in brain specimens with elevated levels of Aβ. The molecule is comprised of a fluorene (a molecule with high affinity for Aβ) and a nitroxide spin label (a paramagnetic MRI contrast species). Labeling of brain specimens with the spin-labeled fluorene produces negative contrast in samples from AD model mice whereas no negative contrast is seen in specimens harvested from wild-type mice. Injection of spin-labeled fluorene into live mice resulted in good brain penetration, with the compound able to generate contrast 24-h post injection. These results provide a proof of concept method that can be used for early, noninvasive, gadolinium-free detection of amyloid plaques by MRI.
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Affiliation(s)
- Silvia Hilt
- Department of Biochemistry & Molecular Medicine, University of California Davis, Sacramento, CA, USA
| | - Tang Tang
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Jeffrey H Walton
- UCD NMR Facility & and Biomedical Engineering Graduate Group, University of California Davis, Davis, CA, USA
| | - Madhu Budamagunta
- Department of Biochemistry & Molecular Medicine, University of California Davis, Sacramento, CA, USA
| | - Izumi Maezawa
- M.I.N.D. Institute and Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, Pécs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, Pécs, Hungary
| | - Vikrant Singh
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Heike Wulff
- Department of Pharmacology, University of California Davis, Davis, CA, USA
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California Davis, Davis, CA, USA
| | - Lee-Way Jin
- M.I.N.D. Institute and Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, USA
| | - Angelique Louie
- Department of Biomedical Engineering and Chemistry Graduate Group, University of California Davis, Davis, CA, USA
| | - John C Voss
- Department of Biochemistry & Molecular Medicine, University of California Davis, Sacramento, CA, USA
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Hilt S, Rojalin T, Viitala T, Koivuniemi A, Bunker A, Hogiu SW, Kálai T, Hideg K, Yliperttula M, Voss JC. Oligomerization Alters Binding Affinity Between Amyloid Beta and a Modulator of Peptide Aggregation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2017; 121:23974-23987. [PMID: 30214656 PMCID: PMC6130836 DOI: 10.1021/acs.jpcc.7b06164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The soluble oligomeric form of the amyloid beta (Aβ) peptide is the major causative agent in the molecular pathogenesis of Alzheimer's disease (AD). We have previously developed a pyrroline-nitroxyl fluorene compound (SLF) that blocks the toxicity of Aβ. Here we introduce the multi-parametric surface plasmon resonance (MP-SPR) approach to quantify SLF binding and effect on the self-association of the peptide via a label-free, real-time approach. Kinetic analysis of SLF binding to Aβ and measurements of layer thickness alterations inform on the mechanism underlying the ability of SLF to inhibit Aβ toxicity and its progression towards larger oligomeric assemblies. Depending on the oligomeric state of Aβ, distinct binding affinities for SLF are revealed. The Aβ monomer and dimer uniquely possess sub-nanomolar affinity for SLF via a non-specific mode of binding. SLF binding is weaker in oligomeric Aβ, which displays an affinity for SLF on the order of 100 μM. To complement these experiments we carried out molecular docking and molecular dynamics simulations to explore how SLF interacts with the Aβ peptide. The MP-SPR results together with in silico modeling provide affinity data for the SLF-Aβ interaction and allow us to develop a new general method for examining protein aggregation.
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Affiliation(s)
- Silvia Hilt
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Tatu Rojalin
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Tapani Viitala
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Artturi Koivuniemi
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Alex Bunker
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Sebastian Wachsmann Hogiu
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Intellectual Ventures/Global Good, Bellevue, WA, USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Marjo Yliperttula
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
- Department of Pharmaceutical Sciences, University of Padova, Italy
| | - John C. Voss
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
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