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Kasapoğlu KN, Sus N, Kruger J, Frank J, Özçelik B. Fabrication of phenolic loaded spray-dried nanoliposomes stabilized by chitosan and whey protein: Digestive stability, transepithelial transport and bioactivity retention of phenolics. Int J Biol Macromol 2024; 271:132676. [PMID: 38821805 DOI: 10.1016/j.ijbiomac.2024.132676] [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: 02/18/2024] [Revised: 05/18/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
Low bioavailability of phenolic compounds (phenolics) results in low in vivo bioactivity, thus their co-encapsulation could enhance potential health benefits. In this study, reconstitutable nanoliposomes loaded with phenolics varying in solubility were fabricated using spray drying after stabilized by chitosan (CH) or whey protein (WP). The physicochemical properties, biocompatibility, digestive fate, and bioactivity retention of phenolics in different forms were investigated. The surface charge of nanoliposomes (NL) shifted from -18.7 mV to positive due to conjugation with cationic CH (53.1 mV) and WP (14 mV) after spray drying while it was -26.6 mV for only spray-dried phenolics (SDP). Encapsulation efficiency of the tested phenolics ranged between 64.7 % and 95.1 %. Simulated gastrointestinal digestion/Caco-2 cell model was used to estimate the digestive fate of the phenolics yielding up to 3-fold higher bioaccessibility for encapsulated phenolics compared to their native form, combined or individually. However, the cellular uptake or transepithelial transport of phenolics did not differ significantly among formulations, except trans-resveratrol in WP-NL. On the contrary, the suppressive effect of phenolics on fatty acid induced hepatocellular lipid accumulation was strongly dependent on the encapsulation method, no activity was retained by SDP. These findings suggested that reconstitutable nanoliposomes can improve the absorption of phenolics by facilitating their bioaccessibility and thermal and/or processing stability during spray drying.
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Affiliation(s)
- Kadriye Nur Kasapoğlu
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey; Department of Food Biofunctionality (140b), Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 28, 70599 Stuttgart, Germany.
| | - Nadine Sus
- Department of Food Biofunctionality (140b), Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 28, 70599 Stuttgart, Germany.
| | - Johanita Kruger
- Department of Food Biofunctionality (140b), Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 28, 70599 Stuttgart, Germany.
| | - Jan Frank
- Department of Food Biofunctionality (140b), Institute of Nutritional Sciences, University of Hohenheim, Garbenstraße 28, 70599 Stuttgart, Germany.
| | - Beraat Özçelik
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey; BIOACTIVE Research & Innovation Food Manufacturing Industry Trade LTD Co, 34469 Maslak, Istanbul, Turkey.
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2
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Mythri RB, Aishwarya MRB. Biopolymers as promising vehicles for drug delivery to the brain. Drug Metab Rev 2024; 56:46-61. [PMID: 37955126 DOI: 10.1080/03602532.2023.2281855] [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: 05/31/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
The brain is a privileged organ, tightly guarded by a network of endothelial cells, pericytes, and glial cells called the blood brain barrier. This barrier facilitates tight regulation of the transport of molecules, ions, and cells from the blood to the brain. While this feature ensures protection to the brain, it also presents a challenge for drug delivery for brain diseases. It is, therefore, crucial to identify molecules and/or vehicles that carry drugs, cross the blood brain barrier, and reach targets within the central nervous system. Biopolymers are large polymeric molecules obtained from biological sources. In comparison with synthetic polymers, biopolymers are structurally more complex and their 3D architecture makes them biologically active. Researchers are therefore investigating biopolymers as safe and efficient carriers of brain-targeted therapeutic agents. In this article, we bring together various approaches toward achieving this objective with a note on the prospects for biopolymer-based neurotherapeutic/neurorestorative/neuroprotective interventions. Finally, as a representative paradigm, we discuss the potential use of nanocarrier biopolymers in targeting protein aggregation diseases.
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Affiliation(s)
- Rajeswara Babu Mythri
- Department of Psychology, Christ (Deemed to be University), Dharmaram College Post, Bengaluru, Karnataka, India
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3
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Impaired Extracellular Proteostasis in Patients with Heart Failure. Arch Med Res 2023; 54:211-222. [PMID: 36797157 DOI: 10.1016/j.arcmed.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 01/11/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Proteostasis impairment and the consequent increase of amyloid burden in the myocardium have been associated with heart failure (HF) development and poor prognosis. A better knowledge of the protein aggregation process in biofluids could assist the development and monitoring of tailored interventions. AIM To compare the proteostasis status and protein's secondary structures in plasma samples of patients with HF with preserved ejection fraction (HFpEF), patients with HF with reduced ejection fraction (HFrEF), and age-matched individuals. METHODS A total of 42 participants were enrolled in 3 groups: 14 patients with HFpEF, 14 patients with HFrEF, and 14 age-matched individuals. Proteostasis-related markers were analyzed by immunoblotting techniques. Fourier Transform Infrared (FTIR) Spectroscopy in Attenuated Total Reflectance (ATR) was applied to assess changes in the protein's conformational profile. RESULTS Patients with HFrEF showed an elevated concentration of oligomeric proteic species and reduced clusterin levels. ATR-FTIR spectroscopy coupled with multivariate analysis allowed the discrimination of HF patients from age-matched individuals in the protein amide I absorption region (1700-1600 cm-1), reflecting changes in protein conformation, with a sensitivity of 73 and a specificity of 81%. Further analysis of FTIR spectra showed significantly reduced random coils levels in both HF phenotypes. Also, compared to the age-matched group, the levels of structures related to fibril formation were significantly increased in patients with HFrEF, whereas the β-turns were significantly increased in patients with HFpEF. CONCLUSION Both HF phenotypes showed a compromised extracellular proteostasis and different protein conformational changes, suggesting a less efficient protein quality control system.
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4
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Mass spectrometric insights into protein aggregation. Essays Biochem 2023; 67:243-253. [PMID: 36636963 PMCID: PMC10070474 DOI: 10.1042/ebc20220103] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
Abstract
Protein aggregation is now recognized as a generic and significant component of the protein energy landscape. Occurring through a complex and dynamic pathway of structural interconversion, the assembly of misfolded proteins to form soluble oligomers and insoluble aggregates remains a challenging topic of study, both in vitro and in vivo. Since the etiology of numerous human diseases has been associated with protein aggregation, and it has become a field of increasing importance in the biopharmaceutical industry, the biophysical characterization of protein misfolded states and their aggregation mechanisms continues to receive increased attention. Mass spectrometry (MS) has firmly established itself as a powerful analytical tool capable of both detection and characterization of proteins at all levels of structure. Given inherent advantages of biological MS, including high sensitivity, rapid timescales of analysis, and the ability to distinguish individual components from complex mixtures with unrivalled specificity, it has found widespread use in the study of protein aggregation, importantly, where traditional structural biology approaches are often not amenable. The present review aims to provide a brief overview of selected MS-based approaches that can provide a range of biophysical descriptors associated with protein conformation and the aggregation pathway. Recent examples highlight where this technology has provided unique structural and mechanistic understanding of protein aggregation.
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5
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Estaun-Panzano J, Arotcarena ML, Bezard E. Monitoring α-synuclein aggregation. Neurobiol Dis 2023; 176:105966. [PMID: 36527982 PMCID: PMC9875312 DOI: 10.1016/j.nbd.2022.105966] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Synucleinopathies, including Parkinson's disease (PD), dementia with Lewy Bodies (DLB), and multiple system atrophy (MSA), are characterized by the misfolding and subsequent aggregation of alpha-synuclein (α-syn) that accumulates in cytoplasmic inclusions bodies in the cells of affected brain regions. Since the seminal report of likely-aggregated α-syn presence within the Lewy bodies by Spillantini et al. in 1997, the keyword "synuclein aggregation" has appeared in over 6000 papers (Source: PubMed October 2022). Studying, observing, describing, and quantifying α-syn aggregation is therefore of paramount importance, whether it happens in tubo, in vitro, in post-mortem samples, or in vivo. The past few years have witnessed tremendous progress in understanding aggregation mechanisms and identifying various polymorphs. In this context of growing complexity, it is of utmost importance to understand what tools we possess, what exact information they provide, and in what context they may be applied. Nonetheless, it is also crucial to rationalize the relevance of the information and the limitations of these methods for gauging the final result. In this review, we present the main techniques that have shaped the current views about α-syn structure and dynamics, with particular emphasis on the recent breakthroughs that may change our understanding of synucleinopathies.
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Affiliation(s)
| | | | - Erwan Bezard
- Univ. Bordeaux, CNRS, IMN, UMR 5293, F-33000 Bordeaux, France; Motac Neuroscience Ltd, Manchester, United Kingdom.
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6
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Nakagawa Y, Shen HCH, Komi Y, Sugiyama S, Kurinomaru T, Tomabechi Y, Krayukhina E, Okamoto K, Yokoyama T, Shirouzu M, Uchiyama S, Inaba M, Niwa T, Sako Y, Taguchi H, Tanaka M. Amyloid conformation-dependent disaggregation in a reconstituted yeast prion system. Nat Chem Biol 2022; 18:321-331. [PMID: 35177839 DOI: 10.1038/s41589-021-00951-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 11/23/2021] [Indexed: 01/17/2023]
Abstract
Disaggregation of amyloid fibrils is a fundamental biological process required for amyloid propagation. However, due to the lack of experimental systems, the molecular mechanism of how amyloid is disaggregated by cellular factors remains poorly understood. Here, we established a robust in vitro reconstituted system of yeast prion propagation and found that heat-shock protein 104 (Hsp104), Ssa1 and Sis1 chaperones are essential for efficient disaggregation of Sup35 amyloid. Real-time imaging of single-molecule fluorescence coupled with the reconstitution system revealed that amyloid disaggregation is achieved by ordered, timely binding of the chaperones to amyloid. Remarkably, we uncovered two distinct prion strain conformation-dependent modes of disaggregation, fragmentation and dissolution. We characterized distinct chaperone dynamics in each mode and found that transient, repeated binding of Hsp104 to the same site of amyloid results in fragmentation. These findings provide a physical foundation for otherwise puzzling in vivo observations and for therapeutic development for amyloid-associated neurodegenerative diseases.
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Affiliation(s)
- Yoshiko Nakagawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | - Howard C-H Shen
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Komi
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | - Shinju Sugiyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan
| | | | - Yuri Tomabechi
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | | | - Kenji Okamoto
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Susumu Uchiyama
- Research Department, U-Medico Inc., Suita, Japan.,Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.,Department of Creative Research, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Japan
| | - Megumi Inaba
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tatsuya Niwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan. .,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
| | - Motomasa Tanaka
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Saitama, Japan. .,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
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7
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Maysinger D, Sanader Maršić Ž, Gran ER, Shobo A, Macairan JR, Zhang I, Perić Bakulić M, Antoine R, Multhaup G, Bonačić-Kouteckỳ V. Insights into the Impact of Gold Nanoclusters Au 10SG 10 on Human Microglia. ACS Chem Neurosci 2022; 13:464-476. [PMID: 35080850 DOI: 10.1021/acschemneuro.1c00621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The purpose of the current study is to uncover the impact of small liganded gold nanoclusters with 10 gold atoms and 10 glutathione ligands (Au10SG10) on several biomarkers in human microglia. We established the links connecting the atomically precise structure of Au10SG10 with their properties and changes in several biomolecules under oxidative stress. Au10SG10 caused the loss of mitochondrial metabolic activity, increased lipid peroxidation and translocation of an alarmin molecule, high mobility group box 1 (HMGB1), from the nucleus to the cytosol. Molecular modeling provided an insight into the location of amino acid interaction sites with Au10SG10 and the nature of bonds participating in these interactions. We show that Au10SG10 can bind directly to the defined sites of reduced, oxidized, and acetylated HMGB1. Further studies with similar complementary approaches merging live-cell analyses, determination of biomarkers, and cell functions could lead to optimized gold nanoclusters best suited for diagnostic and bioimaging purposes in neuroscience.
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Affiliation(s)
- Dusica Maysinger
- Department of Pharmacology & Therapeutics, McGill University, H3G 1Y6 Montréal, Canada
- Interdisciplinary Center for Advanced Science and Technology (ICAST) at University of Split, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Željka Sanader Maršić
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Republic of Croatia
- Interdisciplinary Center for Advanced Science and Technology (ICAST) at University of Split, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Evan Rizzel Gran
- Department of Pharmacology & Therapeutics, McGill University, H3G 1Y6 Montréal, Canada
| | - Adeola Shobo
- Department of Pharmacology & Therapeutics, McGill University, H3G 1Y6 Montréal, Canada
| | - Jun-Ray Macairan
- Department of Chemical Engineering, McGill University, H3A 0C5 Montréal, Canada
| | - Issan Zhang
- Department of Pharmacology & Therapeutics, McGill University, H3G 1Y6 Montréal, Canada
| | - Martina Perić Bakulić
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
- Interdisciplinary Center for Advanced Science and Technology (ICAST) at University of Split, Meštrovićevo šetalište 45, 21000 Split, Croatia
| | - Rodolphe Antoine
- Institut Lumière Matière UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon, F-69100 Villeurbanne, France
| | - Gerhard Multhaup
- Department of Pharmacology & Therapeutics, McGill University, H3G 1Y6 Montréal, Canada
| | - Vlasta Bonačić-Kouteckỳ
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
- Interdisciplinary Center for Advanced Science and Technology (ICAST) at University of Split, Meštrovićevo šetalište 45, 21000 Split, Croatia
- Chemistry Department, Humboldt University of Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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8
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Age-related demethylation of the TDP-43 autoregulatory region in the human motor cortex. Commun Biol 2021; 4:1107. [PMID: 34548609 PMCID: PMC8455575 DOI: 10.1038/s42003-021-02621-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022] Open
Abstract
In amyotrophic lateral sclerosis (ALS), TAR DNA-binding protein 43 (TDP-43), which is encoded by TARDBP, forms aggregates in the motor cortex. This aggregate formation may be triggered by an increase in the TDP-43 level with aging. However, the amount of TDP-43 is autoregulated by alternative splicing of the TARDBP 3′UTR, and how this autoregulation is affected by aging remains to be elucidated. We found that DNA demethylation in the autoregulatory region in the TARDBP 3′UTR reduced alternative splicing and increased TARDBP mRNA expression. Furthermore, in the human motor cortex, we found that this region was demethylated with aging, resulting in increased expression of TARDBP mRNA. The acceleration of DNA demethylation in the motor cortex was associated with the age of ALS onset. In summary, the dysregulation of TDP-43 autoregulation by age-related DNA demethylation in the motor cortex may explain the contribution of aging and motor system selectivity in ALS. In order to assess the effects of aging on the autoregulation of TAR DNA-binding protein 43 (TDP-43) and the potential effects of this on the role of TDP-43 in Amyotrophic Lateral Sclerosis (ALS), Koike et al examined post-mortem motor cortex tissue from ALS patients. They found that DNA demethylation in the autoregulatory region of the TARDBP 3′UTR, which encodes TDP-43, increased with age and was associated with the onset age of ALS and thus could be indicative of a role for dysregulation of TDP-43 autoregulation in ALS pathology.
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9
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Lin LE, Miao K, Qian C, Wei L. High spatial-resolution imaging of label-free in vivo protein aggregates by VISTA. Analyst 2021; 146:4135-4145. [PMID: 33949430 PMCID: PMC8238904 DOI: 10.1039/d1an00060h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Amyloid aggregation, formed by aberrant proteins, is a pathological hallmark for neurodegenerative diseases, including Alzheimer's disease and Huntington's disease. High-resolution holistic mapping of the fine structures from these aggregates should facilitate our understanding of their pathological roles. Here, we achieved label-free high-resolution imaging of the polyQ and the amyloid-beta (Aβ) aggregates in cells and tissues utilizing a sample-expansion stimulated Raman strategy. We further focused on characterizing the Aβ plaques in 5XFAD mouse brain tissues. 3D volumetric imaging enabled visualization of the whole plaques, resolving both the fine protein filaments and the surrounding components. Coupling our expanded label-free Raman imaging with machine learning, we obtained specific segmentation of aggregate cores, peripheral filaments together with cell nuclei and blood vessels by pre-trained convolutional neural network models. Combining with 2-channel fluorescence imaging, we achieved a 6-color holistic view of the same sample. This ability for precise and multiplex high-resolution imaging of the protein aggregates and their micro-environment without the requirement of labeling would open new biomedical applications.
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Affiliation(s)
- Li-En Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
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10
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Shoup D, Roth A, Thapa R, Puchalla J, Rye HS. Development and application of multicolor burst analysis spectroscopy. Biophys J 2021; 120:2192-2204. [PMID: 33831389 DOI: 10.1016/j.bpj.2021.03.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/24/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022] Open
Abstract
The formation and disassembly of macromolecular particles is a ubiquitous and essential feature of virtually all living organisms. Additionally, diseases are often associated with the accumulation and propagation of biologically active nanoparticles, like the formation of toxic protein aggregates in protein misfolding diseases and the growth of infectious viral particles. The heterogeneous and dynamic nature of biologically active particles can make them exceedingly challenging to study. The single-particle fluorescence technique known as burst analysis spectroscopy (BAS) was developed to facilitate real-time measurement of macromolecular particle distributions in the submicron range in a minimally perturbing, free-solution environment. Here, we develop a multicolor version of BAS and employ it to examine two problems in macromolecular assembly: 1) the extent of DNA packing heterogeneity in bacteriophage viral particles and 2) growth models of non-native protein aggregates. We show that multicolor BAS provides a powerful and flexible approach to studying hidden properties of important biological particles like viruses and protein aggregates.
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Affiliation(s)
- Daniel Shoup
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Rajan Thapa
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Jason Puchalla
- Department of Physics, Princeton University, Princeton, New Jersey.
| | - Hays S Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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11
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Kumar H, Udgaonkar JB. The Lys 280 → Gln mutation mimicking disease-linked acetylation of Lys 280 in tau extends the structural core of fibrils and modulates their catalytic properties. Protein Sci 2021; 30:785-803. [PMID: 33496017 DOI: 10.1002/pro.4030] [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: 11/06/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
Amyloid fibrillar aggregates isolated from the brains of patients with neurodegenerative diseases invariably have post-translational modifications (PTMs). The roles that PTMs play in modulating the structures and polymorphism of amyloid aggregates, and hence their ability to catalyze the conversion of monomeric protein to their fibrillar structure is, however, poorly understood. This is particularly true in the case of tau aggregates, where specific folds of fibrillar tau have been implicated in specific tauopathies. Several PTMs, including acetylation at Lys 280, increase aggregation of tau in the brain, and increase neurodegeneration. In this study, tau-K18 K280Q, in which the Lys 280 → Gln mutation is used to mimic acetylation at Lys 280, is shown, using HX-MS measurements, to form fibrils with a structural core that is longer than that of tau-K18 fibrils. Measurements of critical concentrations show that the binding affinity of monomeric tau-K18 for its fibrillar counterpart is only marginally more than that of monomeric tau-K18 K280Q for its fibrillar counterpart. Quantitative analysis of the kinetics of seeded aggregation, using a simple Michaelis-Menten-like model, in which the monomer first binds and then undergoes conformational conversion to β-strand, shows that the fibrils of tau-K18 K280Q convert monomeric protein more slowly than do fibrils of tau-K18. In contrast, monomeric tau-K18 K280Q is converted faster to fibrils than is monomeric tau-K18. Thus, the effect of Lys 280 acetylation on tau aggregate propagation in brain cells is expected to depend on the amount of acetylated tau present, and on whether the propagating seed is acetylated at Lys 280 or not.
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Affiliation(s)
- Harish Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.,Indian Institute of Science Education and Research, Pune, India
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12
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Jung KH, Zhang X. Fluorogenic detection of protein aggregates in live cells using the AggTag method. Methods Enzymol 2020; 639:1-22. [PMID: 32475397 DOI: 10.1016/bs.mie.2020.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein aggregation is a process that occurs through the self-assembly of misfolded proteins to form soluble oligomers and insoluble aggregates. While there has been significant interest in protein aggregation for neurodegenerative diseases, progress in this field of research has been limited by the lack of effective methods to detect and interrogate these species in live cells. To resolve this issue, we have developed a new imaging method named the AggTag to report on protein aggregation in live cells with fluorescence microscopy. The AggTag method utilizes a genetic fusion of a protein of interest (POI) to a protein tag to conjugate with the AggTag probe, which contains a fluorophore that turns on its fluorescence upon interaction with protein aggregates. Unlike the conventional methods, this method enables one to detect soluble misfolded oligomers that were previously invisible. Furthermore, the AggTag method has been applied for the simultaneous detection of co-aggregation between two different POIs by a dual-color and orthogonal tagging system. This chapter aims to provide step-by-step procedures of the AggTag method for researchers who intend to study aggregation of POIs in mammalian cell lines.
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Affiliation(s)
- Kwan Ho Jung
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Xin Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States.
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13
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Shida T, Kamatari YO, Yoda T, Yamaguchi Y, Feig M, Ohhashi Y, Sugita Y, Kuwata K, Tanaka M. Short disordered protein segment regulates cross-species transmission of a yeast prion. Nat Chem Biol 2020; 16:756-765. [PMID: 32284601 DOI: 10.1038/s41589-020-0516-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Soluble prion proteins contingently encounter foreign prion aggregates, leading to cross-species prion transmission. However, how its efficiency is regulated by structural fluctuation of the host soluble prion protein remains unsolved. In the present study, through the use of two distantly related yeast prion Sup35 proteins, we found that a specific conformation of a short disordered segment governs interspecies prion transmissibility. Using a multidisciplinary approach including high-resolution NMR and molecular dynamics simulation, we identified critical residues within this segment that allow interspecies prion transmission in vitro and in vivo, by locally altering dynamics and conformation of soluble prion proteins. Remarkably, subtle conformational differences caused by a methylene group between asparagine and glutamine sufficed to change the short segment structure and substantially modulate the cross-seeding activity. Thus, our findings uncover how conformational dynamics of the short segment in the host prion protein impacts cross-species prion transmission. More broadly, our study provides mechanistic insights into cross-seeding between heterologous proteins.
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Affiliation(s)
- Toshinobu Shida
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan
| | - Yuji O Kamatari
- Life Science Research Center, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Takao Yoda
- Nagahama Institute of Bio-Science and Technology, Nagahama, Japan.,Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai, Japan.,RIKEN-Max Planck Joint Research Center, Wako, Japan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Yumiko Ohhashi
- Graduate School of Science, Kobe University, Kobe, Japan.,Department of Applied Chemistry, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Research Center for Computational Science, Kobe, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Motomasa Tanaka
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan. .,Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Japan.
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14
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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15
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Gupta A, Mahalakshmi R. Single-residue physicochemical characteristics kinetically partition membrane protein self-assembly and aggregation. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49878-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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16
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Gupta A, Mahalakshmi R. Single-residue physicochemical characteristics kinetically partition membrane protein self-assembly and aggregation. J Biol Chem 2019; 295:1181-1194. [PMID: 31844019 PMCID: PMC6996891 DOI: 10.1074/jbc.ra119.011342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/11/2019] [Indexed: 11/06/2022] Open
Abstract
Ninety-five percent of all transmembrane proteins exist in kinetically trapped aggregation-prone states that have been directly linked to neurodegenerative diseases. Interestingly, the primary sequence almost invariably avoids off-pathway aggregate formation, by folding reliably into its native, thermodynamically stabilized structure. However, with the rising incidence of protein aggregation diseases, it is now important to understand the underlying mechanism(s) of membrane protein aggregation. Micromolecular physicochemical and biochemical alterations in the primary sequence that trigger the formation of macromolecular cross-β aggregates can be measured only through combinatorial spectroscopic experiments. Here, we developed spectroscopic thermal perturbation with 117 experimental variables to assess how subtle protein sequence variations drive the molecular transition of the folded protein to oligomeric aggregates. Using the Yersinia pestis outer transmembrane β-barrel Ail as a model, we delineated how a single-residue substitution that alters the membrane-anchoring ability of Ail significantly contributes to the kinetic component of Ail stability. We additionally observed a stabilizing role for interface aliphatics, and that interface aromatics physicochemically contribute to Ail self-assembly and aggregation. Moreover, our method identified the formation of structured oligomeric intermediates during Ail aggregation. We show that the self-aggregation tendency of Ail is offset by the evolution of a thermodynamically compromised primary sequence that balances folding, stability, and oligomerization. Our approach provides critical information on how subtle changes in protein primary sequence trigger cross-β fibril formation, with insights that have direct implications for deducing the molecular progression of neurodegeneration and amyloidogenesis in humans.
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Affiliation(s)
- Ankit Gupta
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India
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17
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Kumar V, Kumar PG, Yadav JK. Impact of semen-derived amyloid (SEVI) on sperm viability and motility: its implication in male reproductive fitness. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:659-671. [PMID: 31392382 DOI: 10.1007/s00249-019-01391-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/13/2018] [Accepted: 07/29/2019] [Indexed: 01/09/2023]
Abstract
Human semen contains a large number of macromolecules, including proteins/enzymes and carbohydrates, regulating and protecting sperm cells. Proteomic analysis of human seminal fluid led to the discovery of semen amyloids derived from short peptide fragments of the proteins prostatic acid phosphatase (PAP) and semenogelin (SG) which are known to play a crucial role in enhancing HIV infection. However, the relevance of their existence in human semen and role in maintaining sperm behavior remains unclear. Distinct physiological, biochemical, and biophysical attributes might cause these amyloids to influence sperm behavior positively or negatively, affecting fertilization or other reproductive processes. We assessed the direct effect of amyloids derived from a PAP248-286 fragment, on sperm motility and viability, which are crucial parameters for assessment of sperm quality in semen. Co-incubation of human sperm with PAP248-286 amyloids at normal physiological concentrations formed in buffer led to significant reduction in sperm viability, though approximately a 10× higher concentration was needed to show a similar effect with amyloid formed in seminal fluid. Both forms of PAP248-286 amyloid also had a significant impact on sperm motility at physiological levels, in agreement with a previous report. Our study suggests that PAP248-286 amyloids can directly influence sperm motility and viability in a concentration-dependent manner. We hypothesise that the direct toxic effect of PAP248-286 amyloid is normally mitigated by other seminal fluid ingredients, but that in pathological conditions, where PAP248-286 concentrations are elevated and it plays a role in determining sperm health and viability, with relevance for male fertility as well as sterility.
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Affiliation(s)
- Vijay Kumar
- Department of Biotechnology, Central University of Rajasthan, NH-8 Jaipur-Ajmer Highway, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Pradeep G Kumar
- Molecular Reproduction Division, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Jay Kant Yadav
- Department of Biotechnology, Central University of Rajasthan, NH-8 Jaipur-Ajmer Highway, Bandarsindri, Kishangarh, Ajmer, Rajasthan, 305817, India.
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18
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Vus K, Girych M, Trusova V, Gorbenko G, Kurutos A, Vasilev A, Gadjev N, Deligeorgiev T. Cyanine dyes derived inhibition of insulin fibrillization. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Metastable states of HYPK-UBA domain's seeds drive the dynamics of its own aggregation. Biochim Biophys Acta Gen Subj 2018; 1862:2846-2861. [DOI: 10.1016/j.bbagen.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/31/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022]
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20
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Molecular basis for diversification of yeast prion strain conformation. Proc Natl Acad Sci U S A 2018; 115:2389-2394. [PMID: 29467288 DOI: 10.1073/pnas.1715483115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Self-propagating β-sheet-rich fibrillar protein aggregates, amyloid fibers, are often associated with cellular dysfunction and disease. Distinct amyloid conformations dictate different physiological consequences, such as cellular toxicity. However, the origin of the diversity of amyloid conformation remains unknown. Here, we suggest that altered conformational equilibrium in natively disordered monomeric proteins leads to the adaptation of alternate amyloid conformations that have different phenotypic effects. We performed a comprehensive high-resolution structural analysis of Sup35NM, an N-terminal fragment of the Sup35 yeast prion protein, and found that monomeric Sup35NM harbored latent local compact structures despite its overall disordered conformation. When the hidden local microstructures were relaxed by genetic mutations or solvent conditions, Sup35NM adopted a strikingly different amyloid conformation, which redirected chaperone-mediated fiber fragmentation and modulated prion strain phenotypes. Thus, dynamic conformational fluctuations in natively disordered monomeric proteins represent a posttranslational mechanism for diversification of aggregate structures and cellular phenotypes.
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21
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Bou-Nader C, Pecqueur L, Cornu D, Lombard M, Dezi M, Nicaise M, Velours C, Fontecave M, Hamdane D. Power of protein/tRNA functional assembly against aberrant aggregation. Phys Chem Chem Phys 2017; 19:28014-28027. [PMID: 29034944 DOI: 10.1039/c7cp05599d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the mechanisms of protein oligomerization and aggregation is a major concern for biotechnology and medical purposes. However, significant challenges remain in determining the mechanism of formation of these superstructures and the environmental factors that can precisely modulate them. Notably the role that a functional ligand plays in the process of protein aggregation is largely unexplored. We herein address these issues with an original flavin-dependent RNA methyltransferase (TrmFO) used as a protein model since this protein employs a complex set of cofactors and ligands for catalysis. Here, we show that TrmFO carries an unstable protein structure that can partially mis-unfold leading to either formation of irregular and nonfunctional soluble oligomers endowed with hyper-thermal stability or large amorphous aggregates in the presence of salts. Mutagenesis confirmed that this peculiarity is an intrinsic property of a polypeptide and it is independent of the flavin coenzyme. Structural characterization and kinetic studies identified several regions of the protein that enjoy conformational changes and more particularly pinpointed the N-terminal subdomain as being a key element in the mechanisms of oligomerization and aggregation. Only stabilization of this region via tRNA suppresses these aberrant protein states. Although protein chaperones emerged as major actors against aggregation, our study emphasizes that other powerful mechanisms exist such as the stabilizing effect of functional assemblies that provide an additional layer of protection against the instability of the proteome.
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Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, Université Pierre et marie Curie, 11 place Marcelin Berthelot, 75231 Paris Cedex 05, France.
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22
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Rasouli S, Abdolvahabi A, Croom CM, Plewman DL, Shi Y, Ayers JI, Shaw BF. Lysine acylation in superoxide dismutase-1 electrostatically inhibits formation of fibrils with prion-like seeding. J Biol Chem 2017; 292:19366-19380. [PMID: 28974578 DOI: 10.1074/jbc.m117.805283] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/28/2017] [Indexed: 11/06/2022] Open
Abstract
The acylation of lysine residues in superoxide dismutase-1 (SOD1) has been previously shown to decrease its rate of nucleation and elongation into amyloid-like fibrils linked to amyotrophic lateral sclerosis. The chemical mechanism underlying this effect is unclear, i.e. hydrophobic/steric effects versus electrostatic effects. Moreover, the degree to which the acylation might alter the prion-like seeding of SOD1 in vivo has not been addressed. Here, we acylated a fraction of lysine residues in SOD1 with groups of variable hydrophobicity, charge, and conformational entropy. The effect of each acyl group on the rate of SOD1 fibril nucleation and elongation were quantified in vitro with thioflavin-T (ThT) fluorescence, and we performed 594 iterate aggregation assays to obtain statistically significant rates. The effect of the lysine acylation on the prion-like seeding of SOD1 was assayed in spinal cord extracts of transgenic mice expressing a G85R SOD1-yellow fluorescent protein construct. Acyl groups with >2 carboxylic acids diminished self-assembly into ThT-positive fibrils and instead promoted the self-assembly of ThT-negative fibrils and amorphous complexes. The addition of ThT-negative, acylated SOD1 fibrils to organotypic spinal cord failed to produce the SOD1 inclusion pathology that typically results from the addition of ThT-positive SOD1 fibrils. These results suggest that chemically increasing the net negative surface charge of SOD1 via acylation can block the prion-like propagation of oligomeric SOD1 in spinal cord.
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Affiliation(s)
- Sanaz Rasouli
- From the Department of Chemistry and Biochemistry and.,the Institute of Biomedical Studies, Baylor University, Waco, Texas 76706 and
| | | | | | | | - Yunhua Shi
- From the Department of Chemistry and Biochemistry and
| | - Jacob I Ayers
- the Department of Neuroscience, University of Florida, Gainesville, Florida 32611
| | - Bryan F Shaw
- From the Department of Chemistry and Biochemistry and
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23
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Kumar H, Singh J, Kumari P, Udgaonkar JB. Modulation of the extent of structural heterogeneity in α-synuclein fibrils by the small molecule thioflavin T. J Biol Chem 2017; 292:16891-16903. [PMID: 28760825 DOI: 10.1074/jbc.m117.795617] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/15/2017] [Indexed: 12/18/2022] Open
Abstract
The transition of intrinsically disordered, monomeric α-synuclein into β-sheet-rich oligomers and fibrils is associated with multiple neurodegenerative diseases. Fibrillar aggregates possessing distinct structures that differ in toxicity have been observed in different pathological phenotypes. Understanding the mechanism of the formation of various fibril polymorphs with differing cytotoxic effects is essential for determining how the aggregation reaction could be modulated to favor nontoxic fibrils over toxic fibrils. In this study, two morphologically different α-synuclein fibrils, one helical and the other ribbon-like, are shown to form together. Surprisingly, a widely used small molecule for probing aggregation reactions, thioflavin T (ThT), was found to tune the structural heterogeneity found in the fibrils. The ribbon-like fibrils formed in the presence of ThT were found to have a longer structural core than the helical fibrils formed in the absence of ThT. The ribbon-like fibrils are also more toxic to cells. By facilitating the formation of ribbon-like fibrils over helical fibrils, ThT reduced the extent of fibril polymorphism. This study highlights the role of a small molecule such as ThT in selectively favoring the formation of a specific type of fibril by binding to aggregates formed early on one of multiple pathways, thereby altering the structural core and external morphology of the fibrils formed.
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Affiliation(s)
- Harish Kumar
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jogender Singh
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,the Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, and
| | - Pratibha Kumari
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,the Laboratory of Physical Chemistry, Hönggerberg Campus, ETH Zurich, 8093 Zurich, Switzerland
| | - Jayant B Udgaonkar
- From the National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India,
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24
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Mitochondrial dysfunction induced by a SH2 domain-targeting STAT3 inhibitor leads to metabolic synthetic lethality in cancer cells. Proc Natl Acad Sci U S A 2017; 114:E4924-E4933. [PMID: 28584133 DOI: 10.1073/pnas.1615730114] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In addition to its canonical role in nuclear transcription, signal transducer and activator of transcription 3 (STAT3) is emerging as an important regulator of mitochondrial function. Here, we demonstrate that a novel inhibitor that binds with high affinity to the STAT3 SH2 domain triggers a complex cascade of events initiated by interference with mitochondrial STAT3 (mSTAT3). The mSTAT3-drug interaction leads to mitochondrial dysfunction, accumulation of proteotoxic STAT3 aggregates, and cell death. The cytotoxic effects depend directly on the drug's ability to interfere with mSTAT3 and mitochondrial function, as demonstrated by site-directed mutagenesis and use of STAT3 knockout and mitochondria-depleted cells. Importantly, the lethal consequences of mSTAT3 inhibition are enhanced by glucose starvation and by increased reliance of cancer cells and tumor-initiating cells on mitochondria, resulting in potent activity in cell cultures and tumor xenografts in mice. These findings can be exploited for eliciting synthetic lethality in metabolically stressed cancer cells using high-affinity STAT3 inhibitors. Thus, this study provides insights on the role of mSTAT3 in cancer cells and a conceptual framework for developing more effective cancer therapies.
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25
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Mukherjee J, Gupta MN. Protein aggregates: Forms, functions and applications. Int J Biol Macromol 2017; 97:778-789. [DOI: 10.1016/j.ijbiomac.2016.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 11/02/2016] [Accepted: 11/05/2016] [Indexed: 11/15/2022]
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26
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Hu ZW, Ma MR, Chen YX, Zhao YF, Qiang W, Li YM. Phosphorylation at Ser 8 as an Intrinsic Regulatory Switch to Regulate the Morphologies and Structures of Alzheimer's 40-residue β-Amyloid (Aβ40) Fibrils. J Biol Chem 2017; 292:2611-2623. [PMID: 28031462 PMCID: PMC5314160 DOI: 10.1074/jbc.m116.757179] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 12/05/2016] [Indexed: 01/23/2023] Open
Abstract
Polymorphism of amyloid-β (Aβ) fibrils, implying different fibril structures, may play important pathological roles in Alzheimer's disease (AD). Morphologies of Aβ fibrils were found to be sensitive to fibrillation conditions. Herein, the Ser8-phosphorylated Aβ (pAβ), which is assumed to specially associate with symptomatic AD, is reported to modify the morphology, biophysical properties, cellular toxicity, and structures of Aβ fibrils. Under the same fibrillation conditions, pAβ favors the formation of fibrils (Fpβ), which are different from the wild-type Aβ fibrils (Fβ). Both Fβ and Fpβ fibrils show single predominant morphologies. Compared with Fβ, Fpβ exhibits higher propagation efficiency and higher neuronal cell toxicity. The residue-specific structural differences between the Fβ- and Fpβ-seeded Aβ fibrils were identified using magic angle spin NMR. Our results suggest a potential regulatory mechanism of phosphorylation on Aβ fibril formation in AD and imply that the post-translationally modified Aβ, especially the phosphorylated Aβ, may be an important target for the diagnosis or treatment of AD at specific stages.
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Affiliation(s)
- Zhi-Wen Hu
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Meng-Rong Ma
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yong-Xiang Chen
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yu-Fen Zhao
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, New York 13902, and
| | - Yan-Mei Li
- From the Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China,
- Beijing Institute for Brain Disorders, Beijing 100069, China
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27
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Ranganathan S, Maji SK, Padinhateeri R. Defining a Physical Basis for Diversity in Protein Self-Assemblies Using a Minimal Model. J Am Chem Soc 2016; 138:13911-13922. [DOI: 10.1021/jacs.6b06433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Srivastav Ranganathan
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Samir K. Maji
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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28
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A Decentralized Approach to the Formulation of Hypotheses: A Hierarchical Structural Model for a Prion Self-Assembled System. Sci Rep 2016; 6:30633. [PMID: 27464832 PMCID: PMC4964355 DOI: 10.1038/srep30633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/06/2016] [Indexed: 11/13/2022] Open
Abstract
Innovation in hypotheses is a key transformative driver for scientific development.
The conventional centralized hypothesis formulation approach, where a dominant
hypothesis is typically derived from a primary phenomenon, can, inevitably, impose
restriction on the range of conceivable experiments and legitimate hypotheses, and
ultimately impede understanding of the system of interest. We report herein the
proposal of a decentralized approach for the formulation of hypotheses, through
initial preconception-free phenomenon accumulation and subsequent reticular logical
reasoning processes. The two-step approach can provide an unbiased, panoramic view
of the system and as such should enable the generation of a set of more coherent and
therefore plausible hypotheses. As a proof-of-concept demonstration of the utility
of this open-ended approach, a hierarchical model has been developed for a prion
self-assembled system, allowing insight into hitherto elusive static and dynamic
features associated with this intriguing structure.
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29
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Ranganathan S, Ghosh D, Maji SK, Padinhateeri R. A minimal conformational switching-dependent model for amyloid self-assembly. Sci Rep 2016; 6:21103. [PMID: 26883720 PMCID: PMC4756677 DOI: 10.1038/srep21103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/19/2016] [Indexed: 11/14/2022] Open
Abstract
Amyloid formation is associated with various pathophysiological conditions like Alzheimer’s and Parkinson’s diseases as well as many useful functions. The hallmark of amyloid assemblies is a conformational transition of the constituent proteins into a β - sheet rich filament. Accounting for this conformational transition in amyloidogenic proteins, we develop an analytically solvable model that can probe the dynamics of an ensemble of single filaments. Using the theory and Monte Carlo simulations, we show the presence of two kinetic regimes for the growth of a self-assembling filament – switching-dependent and –independent growth regimes. We observe a saturation in fibril elongation velocities at higher concentrations in the first regime, providing a novel explanation to the concentration-independence of growth velocities observed experimentally. We also compute the length fluctuation of the filaments to characterize aggregate heterogeneity. From the early velocities and length fluctuation, we propose a novel way of estimating the conformational switching rate. Our theory predicts a kinetic phase diagram that has three distinct phases – short oligomers/monomers, disordered aggregates and β -rich filaments. The model also predicts the force generation potential and the intermittent growth of amyloid fibrils evident from single molecular experiments. Our model could contribute significantly to the physical understanding of amyloid aggregation.
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Affiliation(s)
| | - Dhiman Ghosh
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
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30
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Do TD, de Almeida NEC, LaPointe NE, Chamas A, Feinstein SC, Bowers MT. Amino Acid Metaclusters: Implications of Growth Trends on Peptide Self-Assembly and Structure. Anal Chem 2015; 88:868-76. [PMID: 26632663 DOI: 10.1021/acs.analchem.5b03454] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion-mobility mass spectrometry is utilized to examine the metacluster formation of serine, asparagine, isoleucine, and tryptophan. These amino acids are representative of different classes of noncharged amino acids. We show that they can form relatively large metaclusters in solution that are difficult or impossible to observe by traditional solution techniques. We further demonstrate, as an example, that the formation of Ser metaclusters is not an ESI artifact because large metaclusters can be detected in negative polarity and low concentration with similar cross sections to those measured in positive polarity and higher concentration. The growth trends of tryptophan and isoleucine metaclusters, along with serine, asparagine, and the previously studied phenylalanine, are balanced among various intrinsic properties of individual amino acids (e.g., hydrophobicity, size, and shape). The metacluster cross sections of hydrophilic residues (Ser, Asn, Trp) tend to stay on or fall below the isotropic model trend lines whereas those of hydrophobic amino acids (Ile, Phe) deviate positively from the isotropic trend lines. The growth trends correlate well to the predicted aggregation propensity of individual amino acids. From the metacluster data, we introduce a novel approach to score and predict aggregation propensity of peptides, which can offer a significant improvement over the existing methods in terms of accuracy. Using a set of hexapeptides, we show that the strong negative deviations of Ser metaclusters from the isotropic model leads a prediction of microcrystalline formation for the SFSFSF peptide, whereas the strong positive deviation of Ile leads to prediction or fibril formation for the NININI peptide. Both predictions are confirmed experimentally using ion mobility and TEM measurements. The peptide SISISI is predicted to only weakly aggregate, a prediction confirmed by TEM.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Natália E C de Almeida
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Nichole E LaPointe
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Ali Chamas
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Stuart C Feinstein
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology University of California , Santa Barbara, California 93106, United States
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