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Wang J, Du L, Zhang T, Chu Y, Wang Y, Wang Y, Ji X, Kang Y, Cui R, Zhang G, Liu J, Shi G. Edaravone Dexborneol ameliorates the cognitive deficits of APP/PS1 mice by inhibiting TLR4/MAPK signaling pathway via upregulating TREM2. Neuropharmacology 2024; 255:110006. [PMID: 38763325 DOI: 10.1016/j.neuropharm.2024.110006] [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: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Currently, there are no effective therapeutic agents available to treat Alzheimer's disease (AD). However, edaravone dexborneol (EDB), a novel composite agent used to treat acute ischemic stroke, has recently been shown to exert efficacious neuroprotective effects. However, whether EDB can ameliorate cognitive deficits in AD currently remains unclear. To this end, we explored the effects of EDB on AD and its potential mechanisms using an AD animal model (male APP/PS1 mice) treated with EDB for 10 weeks starting at 6 months of age. Subsequent analyses revealed that EDB-treated APP/PS1 mice exhibited improved cognitive abilities compared to untreated APP/PS1 mice. Administration of EDB in APP/PS1 mice further alleviated neuropathological alterations of the hippocampus, including Aβ deposition, pyramidal cell karyopyknosis, and oxidative damage, and significantly decreased the levels of inflammatory cytokines (IL-1β, IL-6 and TNF-α) and COX-2 in the hippocampus of APP/PS1 mice. Transcriptome sequencing analysis demonstrated the critical role of the inflammatory reaction in EDB treatment in APP/PS1 mice, indicating that the alleviation of the inflammatory reaction by EDB in the hippocampus of APP/PS1 mice was linked to the action of the TREM2/TLR4/MAPK signaling pathway. Further in vitro investigations showed that EDB suppressed neuroinflammation in LPS-stimulated BV2 cells by inhibiting the TLR4/MAPK signaling pathway and upregulating TREM2 expression. Thus, the findings of the present study demonstrate that EDB is a promising therapeutic agent for AD-related cognitive dysfunction.
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Affiliation(s)
- Jinyang Wang
- Department of Neurology, The Third Hospital of Hebei Medical University, Shijiazhuang, 050051, China; Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Longyuan Du
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Tianyun Zhang
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China; Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yun Chu
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yue Wang
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yu Wang
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China; Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, China
| | - Xiaoming Ji
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China; Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yunxiao Kang
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China; Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, China
| | - Rui Cui
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China; Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, China
| | - Guoliang Zhang
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China; Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, China
| | - Junyan Liu
- Department of Neurology, The Third Hospital of Hebei Medical University, Shijiazhuang, 050051, China
| | - Geming Shi
- Laboratory of Neurobiology, Hebei Medical University, Shijiazhuang, 050017, China; Neuroscience Research Center, Hebei Medical University, Shijiazhuang, 050017, China.
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2
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Chaki S, Santra S, Dasgupta S. Fibrillation of Human Serum Albumin Differentially Affected by Asp-, Arg-, and Tyr-Capped Gold Nanoparticles. J Phys Chem B 2024; 128:3538-3553. [PMID: 38507578 DOI: 10.1021/acs.jpcb.3c06932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Fibrillation of proteins is associated with a number of debilitating diseases, including various neurodegenerative disorders. Prevention of the protein fibrillation process is therefore of immense importance. We investigated the effect of amino acid-capped AuNPs on the prevention of the fibrillation process of human serum albumin (HSA), a model protein. Amino acid-capped AuNPs of varying sizes and agglomeration extents were synthesized under physiological conditions. The AuNPs were characterized by their characteristic surface plasmon resonance (SPR), and their interactions with HSA were investigated through emission spectroscopy in addition to circular dichroism (CD) spectral analyses. Fluorescence lifetime imaging (FLIM) as well as transmission electron microscopy (TEM) were used to observe the fibrillar network. Thermodynamic and kinetic analyses from CD and fluorescence emission spectra provided insights into the fibrillation pathway adopted by HSA in the presence of capped AuNPs. Kinetics of the fibrillation pathway followed by ThT fluorescence emission confirmed the sigmoidal nature of the process. The highest cooperativity was observed in the case of Asp-AuNPs with HSA. This was in accordance with the ΔG value obtained from the CD spectral analyses, where Arg-AuNPs with HSA showed the highest positive ΔG value and Asp-AuNPs with HSA showed the most negative ΔG value. The study provides information about the potential use of conjugate AuNPs to monitor the fibrillation process in proteins.
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Affiliation(s)
- Sreshtha Chaki
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sujan Santra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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3
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Geijtenbeek KW, Aranda AS, Sanz AS, Janzen J, Bury AE, Kors S, Al Amery N, Schmitz NCM, Reits EAJ, Schipper-Krom S. Insulin-Degrading Enzyme Efficiently Degrades polyQ Peptides but not Expanded polyQ Huntingtin Fragments. J Huntingtons Dis 2024:JHD230583. [PMID: 38640164 DOI: 10.3233/jhd-230583] [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: 04/21/2024]
Abstract
Background Huntington's disease is an inheritable autosomal dominant disorder caused by an expanded CAG trinucleotide repeat within the Huntingtin gene, leading to a polyglutamine (polyQ) expansion in the mutant protein. Objective A potential therapeutic approach for delaying or preventing the onset of the disease involves enhancing the degradation of the aggregation-prone polyQ-expanded N-terminal mutant huntingtin (mHTT) exon1 fragment. A few proteases and peptidases have been identified that are able to cleave polyQ fragments with low efficiency. This study aims to identify a potent polyQ-degrading endopeptidase. Methods Here we used quenched polyQ peptides to identify a polyQ-degrading endopeptidase. Next we investigated its role on HTT turnover, using purified polyQ-expanded HTT fragments and striatal cells expressing mHTT exon1 peptides. Results We identified insulin-degrading enzyme (IDE) as a novel endopeptidase for degrading polyQ peptides. IDE was, however, ineffective in reducing purified polyQ-expanded HTT fragments. Similarly, in striatal cells expressing mHTT exon1 peptides, IDE did not enhance mHTT turnover. Conclusions This study shows that despite IDE's efficiency in degrading polyQ peptides, it does not contribute to the direct degradation of polyQ-expanded mHTT fragments.
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Affiliation(s)
- Karlijne W Geijtenbeek
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Angela Santiago Aranda
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Alicia Sanz Sanz
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Jolien Janzen
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Aleksandra E Bury
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Suzan Kors
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | | | - Nina C M Schmitz
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Eric A J Reits
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Amsterdam UMC, University of Amsterdam, Medical Biology, Meibergdreef, Amsterdam, Netherlands
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4
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Mishra N, Dubey S, Kumari A, Khan MA, Kuligina ES, Preobrazhenskaya EV, Romanko AA, Yadav LR, Sarin R, Imyanitov EN, Varma AK. Structural implications of amyloidogenic rare variants Ser282Leu and Gln356Arg identified in h-BRCA1. Proteins 2024; 92:540-553. [PMID: 38037760 DOI: 10.1002/prot.26638] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Preliminary studies have shown BRCA1 (170-1600) residues to be intrinsically disordered with unknown structural details. However, thousands of clinically reported variants have been identified in this central region of BRCA1. Therefore, we aimed to characterize h-BRCA1(260-553) to assess the structural basis for pathogenicity of two rare missense variants Ser282Leu, Gln356Arg identified from the Indian and Russian populations respectively. Small-angle X-ray scattering analysis revealed WT scores Rg -32 Å, Dmax -93 Å, and Rflex-51% which are partially disordered, whereas Ser282Leu variant displayed a higher degree of disorderedness and Gln356Arg was observed to be aggregated. WT protein also possesses an inherent propensity to undergo a disorder-to-order transition in the presence of cruciform DNA and 2,2,2-Trifluoroethanol (TFE). An increased alpha-helical pattern was observed with increasing concentration of TFE for the Gln356Arg mutant whereas Ser282Leu mutant showed significant differences only at the highest TFE concentration. Furthermore, higher thermal shift was observed for WT-DNA complex compared to the Gln356Arg and Ser282Leu protein-DNA complex. Moreover, mature amyloid-like fibrils were observed with 30 μM thioflavin T (ThT) at 37°C for Ser282Leu and Gln356Arg proteins while the WT protein exists in a protofibril state as observed by TEM. Gln356Arg formed higher-order aggregates with amyloidogenesis over time as monitored by ThT fluorescence. In addition, computational analyses confirmed larger conformational fluctuations for Ser282Leu and Gln356Arg mutants than for the WT. The global structural alterations caused by these variants provide a mechanistic approach for further classification of the variants of uncertain clinical significance in BRCA1 into amyloidogenic variants which may have a significant role in disease pathogenesis.
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Affiliation(s)
- Neha Mishra
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Suchita Dubey
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Anchala Kumari
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Mudassar Ali Khan
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Ekaterina S Kuligina
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Elena V Preobrazhenskaya
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Alexandr A Romanko
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
| | - Lumbini R Yadav
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
| | - Rajiv Sarin
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Evgeny N Imyanitov
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St. Petersburg, Russia
- Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Center for Treatment, Research and Education in Cancer, Navi Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Mumbai, India
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5
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Sulatskaya AI, Stepanenko OV, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV. Structural determinants of odorant-binding proteins affecting their ability to form amyloid fibrils. Int J Biol Macromol 2024; 264:130699. [PMID: 38460650 DOI: 10.1016/j.ijbiomac.2024.130699] [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: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024]
Abstract
The formation of amyloid fibrils is associated with many severe pathologies as well as the execution of essential physiological functions by proteins. Despite the diversity, all amyloids share a similar morphology and consist of stacked β-strands, suggesting high amyloidogenicity of native proteins enriched with β-structure. Such proteins include those with a β-barrel-like structure with β-strands arranged into a cylindrical β-sheet. However, the mechanisms responsible for destabilization of the native state and triggering fibrillogenesis have not thoroughly explored yet. Here we analyze the structural determinants of fibrillogenesis in proteins with β-barrel structures on the example of odorant-binding protein (OBP), whose amyloidogenicity was recently demonstrated in vitro. We reveal a crucial role in the fibrillogenesis of OBPs for the "open" conformation of the molecule. This conformation is achieved by disrupting the interaction between the β-barrel and the C-terminus of protein monomers or dimers, which exposes "sticky" amyloidogenic sites for interaction. The data suggest that the "open" conformation of OBPs can be induced by destabilizing the native β-barrel structure through the disruption of: 1) intramolecular disulfide cross-linking and non-covalent contacts between the C-terminal fragment and β-barrel in the protein's monomeric form, or 2) intermolecular contacts involved in domain swapping in the protein's dimeric form.
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Affiliation(s)
- Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
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6
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Behera DP, Subadini S, Freudenberg U, Sahoo H. Sulfation of hyaluronic acid reconfigures the mechanistic pathway of bone morphogenetic protein-2 aggregation. Int J Biol Macromol 2024; 263:130128. [PMID: 38350587 DOI: 10.1016/j.ijbiomac.2024.130128] [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: 11/22/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/15/2024]
Abstract
Bone morphogenetic protein-2 (BMP-2) is a critical growth factor of bone extracellular matrix (ECM), pivotal for osteogenesis. Glycosaminoglycans (GAGs), another vital ECM biomolecules, interact with growth factors, affecting signal transduction. Our study primarily focused on hyaluronic acid (HA), a prevalent GAG, and its sulfated derivative (SHA). We explored their impact on BMP-2's conformation, aggregation, and mechanistic pathways of aggregation using diverse optical and rheological methods. In the presence of HA and SHA, the secondary structure of BMP-2 underwent a structured transformation, characterized by a substantial increase in beta sheet content, and a detrimental alteration, manifesting as a shift towards unstructured content, respectively. Although both HA and SHA induced BMP-2 aggregation, their mechanisms differed. SHA led to rapid amorphous aggregates, while HA promoted amyloid fibrils with a lag phase and sigmoidal kinetics. Aggregate size and shape varied; HA produced larger structures, SHA smaller. Each aggregation type followed distinct pathways influenced by viscosity and excluded volume. Higher viscosity, low diffusivity of protein and higher excluded volume In the presence of HA promotes fibrillation having size in micrometer range. Low viscosity, high diffusivity of protein and lesser excluded volume leads to amorphous aggregate of size in nanometer range.
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Affiliation(s)
- Devi Prasanna Behera
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Uwe Freudenberg
- Institute of Polymer Research, Technical University Dresden, 01307 Dresden, Germany
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, National Institute of Technology, Rourkela 769008, Odisha, India; Center for Nanomaterials, National Institute of Technology, Rourkela 769008, Odisha, India.
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7
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Casella C, Ballaz SJ. Genotoxic and neurotoxic potential of intracellular nanoplastics: A review. J Appl Toxicol 2024. [PMID: 38494651 DOI: 10.1002/jat.4598] [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: 02/02/2024] [Revised: 02/18/2024] [Accepted: 02/24/2024] [Indexed: 03/19/2024]
Abstract
Plastic waste comprises polymers of different chemicals that disintegrate into nanoplastic particles (NPLs) of 1-100-nm size, thereby littering the environment and posing a threat to wildlife and human health. Research on NPL contamination has up to now focused on the ecotoxicology effects of the pollution rather than the health risks. This review aimed to speculate about the possible properties of carcinogenic and neurotoxic NPL as pollutants. Given their low-dimensional size and high surface size ratio, NPLs can easily penetrate biological membranes to cause functional and structural damage in cells. Once inside the cell, NPLs can interrupt the autophagy flux of cellular debris, alter proteostasis, provoke mitochondrial dysfunctions, and induce endoplasmic reticulum stress. Harmful metabolic and biological processes induced by NPLs include oxidative stress (OS), ROS generation, and pro-inflammatory reactions. Depending on the cell cycle status, NPLs may direct DNA damage, tumorigenesis, and lately carcinogenesis in tissues with high self-renewal capabilities like epithelia. In cells able to live the longest like neurons, NPLs could trigger neurodegeneration by promoting toxic proteinaceous aggregates, OS, and chronic inflammation. NPL genotoxicity and neurotoxicity are discussed based on the gathered evidence, when available, within the context of the intracellular uptake of these newcomer nanoparticles. In summary, this review explains how the risk evaluation of NPL pollution for human health may benefit from accurately monitoring NPL toxicokinetics and toxicodynamics at the intracellular resolution level.
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Affiliation(s)
- Claudio Casella
- Department Chemical and Environmental Engineering, University of Oviedo, Oviedo, Spain
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8
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James EI, Baggett DW, Chang E, Schachter J, Nixey T, Choi K, Guttman M, Nath A. Tryptanthrin Analogs Substoichiometrically Inhibit Seeded and Unseeded Tau4RD Aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578649. [PMID: 38352474 PMCID: PMC10862865 DOI: 10.1101/2024.02.02.578649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Microtubule-associated protein tau is an intrinsically disordered protein (IDP) that forms characteristic fibrillar aggregates in several diseases, the most well-known of which is Alzheimer's disease (AD). Despite keen interest in disrupting or inhibiting tau aggregation to treat AD and related dementias, there are currently no FDA-approved tau-targeting drugs. This is due, in part, to the fact that tau and other IDPs do not exhibit a single well-defined conformation but instead populate a fluctuating conformational ensemble that precludes finding a stable "druggable" pocket. Despite this challenge, we previously reported the discovery of two novel families of tau ligands, including a class of aggregation inhibitors, identified through a protocol that combines molecular dynamics, structural analysis, and machine learning. Here we extend our exploration of tau druggability with the identification of tryptanthrin and its analogs as potent, substoichiometric aggregation inhibitors, with the best compounds showing potencies in the low nanomolar range even at a ~100-fold molar excess of tau4RD. Moreover, conservative changes in small molecule structure can have large impacts on inhibitory potency, demonstrating that similar structure-activity relationship (SAR) principles as used for traditional drug development also apply to tau and potentially to other IDPs.
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Affiliation(s)
- Ellie I. James
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
| | - David W. Baggett
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Current address: Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Edcon Chang
- Takeda Development Center Americas, San Diego, CA
| | | | - Thomas Nixey
- Takeda Development Center Americas, San Diego, CA
| | | | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
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Area-Gomez E, Schon EA. Towards a Unitary Hypothesis of Alzheimer's Disease Pathogenesis. J Alzheimers Dis 2024; 98:1243-1275. [PMID: 38578892 DOI: 10.3233/jad-231318] [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] [Indexed: 04/07/2024]
Abstract
The "amyloid cascade" hypothesis of Alzheimer's disease (AD) pathogenesis invokes the accumulation in the brain of plaques (containing the amyloid-β protein precursor [AβPP] cleavage product amyloid-β [Aβ]) and tangles (containing hyperphosphorylated tau) as drivers of pathogenesis. However, the poor track record of clinical trials based on this hypothesis suggests that the accumulation of these peptides is not the only cause of AD. Here, an alternative hypothesis is proposed in which the AβPP cleavage product C99, not Aβ, is the main culprit, via its role as a regulator of cholesterol metabolism. C99, which is a cholesterol sensor, promotes the formation of mitochondria-associated endoplasmic reticulum (ER) membranes (MAM), a cholesterol-rich lipid raft-like subdomain of the ER that communicates, both physically and biochemically, with mitochondria. We propose that in early-onset AD (EOAD), MAM-localized C99 is elevated above normal levels, resulting in increased transport of cholesterol from the plasma membrane to membranes of intracellular organelles, such as ER/endosomes, thereby upregulating MAM function and driving pathology. By the same token, late-onset AD (LOAD) is triggered by any genetic variant that increases the accumulation of intracellular cholesterol that, in turn, boosts the levels of C99 and again upregulates MAM function. Thus, the functional cause of AD is upregulated MAM function that, in turn, causes the hallmark disease phenotypes, including the plaques and tangles. Accordingly, the MAM hypothesis invokes two key interrelated elements, C99 and cholesterol, that converge at the MAM to drive AD pathogenesis. From this perspective, AD is, at bottom, a lipid disorder.
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Affiliation(s)
- Estela Area-Gomez
- Department of Neurology, Columbia University, New York, NY, USA
- Centro de Investigaciones Biológicas "Margarita Salas", Spanish National Research Council, Madrid, Spain
| | - Eric A Schon
- Department of Neurology, Columbia University, New York, NY, USA
- Department of Genetics and Development>, Columbia University, New York, NY, USA
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10
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Kang S, Kim M, Sun J, Lee M, Min K. Prediction of Protein Aggregation Propensity via Data-Driven Approaches. ACS Biomater Sci Eng 2023; 9:6451-6463. [PMID: 37844262 DOI: 10.1021/acsbiomaterials.3c01001] [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] [Indexed: 10/18/2023]
Abstract
Protein aggregation occurs when misfolded or unfolded proteins physically bind together and can promote the development of various amyloid diseases. This study aimed to construct surrogate models for predicting protein aggregation via data-driven methods using two types of databases. First, an aggregation propensity score database was constructed by calculating the scores for protein structures in the Protein Data Bank using Aggrescan3D 2.0. Moreover, feature- and graph-based models for predicting protein aggregation have been developed by using this database. The graph-based model outperformed the feature-based model, resulting in an R2 of 0.95, although it intrinsically required protein structures. Second, for the experimental data, a feature-based model was built using the Curated Protein Aggregation Database 2.0 to predict the aggregated intensity curves. In summary, this study suggests approaches that are more effective in predicting protein aggregation, depending on the type of descriptor and the database.
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Affiliation(s)
- Seungpyo Kang
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Minseon Kim
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Jiwon Sun
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Myeonghun Lee
- School of Systems Biomedical Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
| | - Kyoungmin Min
- School of Mechanical Engineering, Soongsil University, 369 Sangdo-ro, Dongjak-gu 06978, Seoul, Republic of Korea
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11
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Han J. Copper trafficking systems in cells: insights into coordination chemistry and toxicity. Dalton Trans 2023; 52:15277-15296. [PMID: 37702384 DOI: 10.1039/d3dt02166a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Transition metal ions, such as copper, are indispensable components in the biological system. Copper ions which primarily exist in two major oxidation states Cu(I) and Cu(II) play crucial roles in various cellular processes including antioxidant defense, biosynthesis of neurotransmitters, and energy metabolism, owing to their inherent redox activity. The disturbance in copper homeostasis can contribute to the development of copper metabolism disorders, cancer, and neurodegenerative diseases, highlighting the significance of understanding the copper trafficking system in cellular environments. This review aims to offer a comprehensive overview of copper homeostatic machinery, with an emphasis on the coordination chemistry of copper transporters and trafficking proteins. While copper chaperones and the corresponding metalloenzymes are thoroughly discussed, we also explore the potential existence of low-molecular-mass metal complexes within cellular systems. Furthermore, we summarize the toxicity mechanisms originating from copper deficiency or accumulation, which include the dysregulation of oxidative stress, signaling pathways, signal transduction, and amyloidosis. This perspective review delves into the current knowledge regarding the intricate aspects of the copper trafficking system, providing valuable insights into potential treatment strategies from the standpoint of bioinorganic chemistry.
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Affiliation(s)
- Jiyeon Han
- Department of Applied Chemistry, University of Seoul, Seoul 02504, Republic of Korea.
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Milyaeva OY, Akentiev AV, Bykov AG, Loglio G, Miller R, Portnaya I, Rafikova AR, Noskov BA. Dynamic Properties of Adsorption Layers of κ-Casein Fibrils. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15268-15274. [PMID: 37867296 DOI: 10.1021/acs.langmuir.3c01950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The dynamic surface properties of native κ-casein solutions and aqueous dispersions of its fibrils differ significantly from the corresponding properties of the systems with globular proteins. The dependence of the dynamic surface elasticity of κ-casein solutions on surface pressure has a local maximum, indicating partial displacement of macromolecules from the proximal region of the surface layer to the distal one. This dependence becomes monotonic for fibril dispersions, similar to the results for dispersions of globular protein fibrils, but unlike the latter case, the surface elasticity close to the steady state reaches values that are approximately four times higher than the data for native protein solutions at the same concentrations.
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Affiliation(s)
- Olga Yu Milyaeva
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - Alexander V Akentiev
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - Alexey G Bykov
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - Giuseppe Loglio
- Institute of Condensed Matter Chemistry and Energy Technology, 16149 Genova, Italy
| | - Reinhard Miller
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - Irina Portnaya
- CryoEM Laboratory of Soft Matter, Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000003, Israel
| | - Anastasiya R Rafikova
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - Boris A Noskov
- Department of Colloid Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia
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13
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Kim Y, Li C, Gu C, Fang Y, Tycksen E, Puri A, Pietka TA, Sivapackiam J, Kidd K, Park SJ, Johnson BG, Kmoch S, Duffield JS, Bleyer AJ, Jackrel ME, Urano F, Sharma V, Lindahl M, Chen YM. MANF stimulates autophagy and restores mitochondrial homeostasis to treat autosomal dominant tubulointerstitial kidney disease in mice. Nat Commun 2023; 14:6493. [PMID: 37838725 PMCID: PMC10576802 DOI: 10.1038/s41467-023-42154-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
Misfolded protein aggregates may cause toxic proteinopathy, including autosomal dominant tubulointerstitial kidney disease due to uromodulin mutations (ADTKD-UMOD), a leading hereditary kidney disease. There are no targeted therapies. In our generated mouse model recapitulating human ADTKD-UMOD carrying a leading UMOD mutation, we show that autophagy/mitophagy and mitochondrial biogenesis are impaired, leading to cGAS-STING activation and tubular injury. Moreover, we demonstrate that inducible tubular overexpression of mesencephalic astrocyte-derived neurotrophic factor (MANF), a secreted endoplasmic reticulum protein, after the onset of disease stimulates autophagy/mitophagy, clears mutant UMOD, and promotes mitochondrial biogenesis through p-AMPK enhancement, thus protecting kidney function in our ADTKD mouse model. Conversely, genetic ablation of MANF in the mutant thick ascending limb tubular cells worsens autophagy suppression and kidney fibrosis. Together, we have discovered MANF as a biotherapeutic protein and elucidated previously unknown mechanisms of MANF in the regulation of organelle homeostasis, which may have broad therapeutic applications to treat various proteinopathies.
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Affiliation(s)
- Yeawon Kim
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Chuang Li
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Chenjian Gu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yili Fang
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Anuradhika Puri
- Department of Chemistry, Washington University, St. Louis, MO, USA
| | - Terri A Pietka
- Nutrition and Geriatrics Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Jothilingam Sivapackiam
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kendrah Kidd
- Section of Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Sun-Ji Park
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bryce G Johnson
- Pfizer Worldwide Research and Development, Inflammation & Immunology, Cambridge, MA, USA
| | - Stanislav Kmoch
- Section of Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Anthony J Bleyer
- Section of Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Fumihiko Urano
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Vijay Sharma
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biomedical Engineering, School of Engineering & Applied Science, Washington University, St. Louis, MO, USA
| | - Maria Lindahl
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ying Maggie Chen
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA.
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14
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Hivare P, Mujmer K, Swarup G, Gupta S, Bhatia D. Endocytic pathways of pathogenic protein aggregates in neurodegenerative diseases. Traffic 2023; 24:434-452. [PMID: 37392160 DOI: 10.1111/tra.12906] [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: 09/20/2022] [Revised: 05/14/2023] [Accepted: 06/11/2023] [Indexed: 07/03/2023]
Abstract
Endocytosis is the fundamental uptake process through which cells internalize extracellular materials and species. Neurodegenerative diseases (NDs) are characterized by a progressive accumulation of intrinsically disordered protein species, leading to neuronal death. Misfolding in many proteins leads to various NDs such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS) and other disorders. Despite the significance of disordered protein species in neurodegeneration, their spread between cells and the cellular uptake of extracellular species is not entirely understood. This review discusses the major internalization mechanisms of the different conformer species of these proteins and their endocytic mechanisms. We briefly introduce the broad types of endocytic mechanisms found in cells and then summarize what is known about the endocytosis of monomeric, oligomeric and aggregated conformations of tau, Aβ, α-Syn, Huntingtin, Prions, SOD1, TDP-43 and other proteins associated with neurodegeneration. We also highlight the key players involved in internalizing these disordered proteins and the several techniques and approaches to identify their endocytic mechanisms. Finally, we discuss the obstacles involved in studying the endocytosis of these protein species and the need to develop better techniques to elucidate the uptake mechanisms of a particular disordered protein species.
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Affiliation(s)
- Pravin Hivare
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Kratika Mujmer
- Center for Brain and Cognitive Sciences, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Gitanjali Swarup
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
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15
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Anthuparambil ND, Girelli A, Timmermann S, Kowalski M, Akhundzadeh MS, Retzbach S, Senft MD, Dargasz M, Gutmüller D, Hiremath A, Moron M, Öztürk Ö, Poggemann HF, Ragulskaya A, Begam N, Tosson A, Paulus M, Westermeier F, Zhang F, Sprung M, Schreiber F, Gutt C. Exploring non-equilibrium processes and spatio-temporal scaling laws in heated egg yolk using coherent X-rays. Nat Commun 2023; 14:5580. [PMID: 37696830 PMCID: PMC10495384 DOI: 10.1038/s41467-023-41202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The soft-grainy microstructure of cooked egg yolk is the result of a series of out-of-equilibrium processes of its protein-lipid contents; however, it is unclear how egg yolk constituents contribute to these processes to create the desired microstructure. By employing X-ray photon correlation spectroscopy, we investigate the functional contribution of egg yolk constituents: proteins, low-density lipoproteins (LDLs), and yolk-granules to the development of grainy-gel microstructure and microscopic dynamics during cooking. We find that the viscosity of the heated egg yolk is solely determined by the degree of protein gelation, whereas the grainy-gel microstructure is controlled by the extent of LDL aggregation. Overall, protein denaturation-aggregation-gelation and LDL-aggregation follows Arrhenius-type time-temperature superposition (TTS), indicating an identical mechanism with a temperature-dependent reaction rate. However, above 75 °C TTS breaks down and temperature-independent gelation dynamics is observed, demonstrating that the temperature can no longer accelerate certain non-equilibrium processes above a threshold value.
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Affiliation(s)
- Nimmi Das Anthuparambil
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Department Physik, Universität Siegen, 57072, Siegen, Germany.
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | | | - Marvin Kowalski
- Department Physik, Universität Siegen, 57072, Siegen, Germany
| | | | - Sebastian Retzbach
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Maximilian D Senft
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | | | - Dennis Gutmüller
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Anusha Hiremath
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Marc Moron
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Özgül Öztürk
- Department Physik, Universität Siegen, 57072, Siegen, Germany
| | | | | | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Amir Tosson
- Department Physik, Universität Siegen, 57072, Siegen, Germany
| | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, 57072, Siegen, Germany.
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16
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Puławski W, Koliński A, Koliński M. Integrative modeling of diverse protein-peptide systems using CABS-dock. PLoS Comput Biol 2023; 19:e1011275. [PMID: 37405984 DOI: 10.1371/journal.pcbi.1011275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
The CABS model can be applied to a wide range of protein-protein and protein-peptide molecular modeling tasks, such as simulating folding pathways, predicting structures, docking, and analyzing the structural dynamics of molecular complexes. In this work, we use the CABS-dock tool in two diverse modeling tasks: 1) predicting the structures of amyloid protofilaments and 2) identifying cleavage sites in the peptide substrates of proteolytic enzymes. In the first case, simulations of the simultaneous docking of amyloidogenic peptides indicated that the CABS model can accurately predict the structures of amyloid protofilaments which have an in-register parallel architecture. Scoring based on a combination of symmetry criteria and estimated interaction energy values for bound monomers enables the identification of protofilament models that closely match their experimental structures for 5 out of 6 analyzed systems. For the second task, it has been shown that CABS-dock coarse-grained docking simulations can be used to identify the positions of cleavage sites in the peptide substrates of proteolytic enzymes. The cleavage site position was correctly identified for 12 out of 15 analyzed peptides. When combined with sequence-based methods, these docking simulations may lead to an efficient way of predicting cleavage sites in degraded proteins. The method also provides the atomic structures of enzyme-substrate complexes, which can give insights into enzyme-substrate interactions that are crucial for the design of new potent inhibitors.
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Affiliation(s)
- Wojciech Puławski
- Bioinformatics Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | | | - Michał Koliński
- Bioinformatics Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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17
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Hafycz JM, Strus E, Naidoo NN. Early and late chaperone intervention therapy boosts XBP1s and ADAM10, restores proteostasis, and rescues learning in Alzheimer's Disease mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541973. [PMID: 37292838 PMCID: PMC10245863 DOI: 10.1101/2023.05.23.541973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative disorder that is pervasive among the aging population. Two distinct phenotypes of AD are deficits in cognition and proteostasis, including chronic activation of the unfolded protein response (UPR) and aberrant Aβ production. It is unknown if restoring proteostasis by reducing chronic and aberrant UPR activation in AD can improve pathology and cognition. Here, we present data using an APP knock-in mouse model of AD and several protein chaperone supplementation paradigms, including a late-stage intervention. We show that supplementing protein chaperones systemically and locally in the hippocampus reduces PERK signaling and increases XBP1s, which is associated with increased ADAM10 and decreased Aβ42. Importantly, chaperone treatment improves cognition which is correlated with increased CREB phosphorylation and BDNF. Together, this data suggests that chaperone treatment restores proteostasis in a mouse model of AD and that this restoration is associated with improved cognition and reduced pathology. One-sentence summary Chaperone therapy in a mouse model of Alzheimer's disease improves cognition by reducing chronic UPR activity.
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18
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Santos TP, Calabrese V, Boehm MW, Baier SK, Shen AQ. Flow-induced alignment of protein nanofibril dispersions. J Colloid Interface Sci 2023; 638:487-497. [PMID: 36758259 DOI: 10.1016/j.jcis.2023.01.105] [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: 11/09/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 02/05/2023]
Abstract
HYPOTHESIS Protein nanofibrils (PNF) resulting from the self-assembly of proteins or peptides can present structural ordering triggered by numerous factors, including the shear flow. We hypothesize that i) depending on the contour length of the PNF and the magnitude of the shear rate applied to the PNF dispersion, they exhibit specific orientation, and ii) it is possible to predict the alignment of PNF by establishing a flow-alignment relationship. Understanding such a relationship is pivotal to improving the fundamental knowledge and application of fibril systems. EXPERIMENTS We use β-lactoglobulin PNF aqueous dispersions with different average contour lengths but equal persistence lengths. We employ simple shear-dominated microfluidic devices with state-of-the-art imaging techniques: flow-induced birefringence (FIB) and micro-particle image velocimetry (μ-PIV), to probe the effect of shear flow on PNF alignment. FINDINGS We provide an empirical relationship connecting the birefringence Δn (quantifying the extent of PNF alignment), and the Péclet number Pe (correlating the shear rate of the flow relative to the rotational diffusion of PNF) to understand the flow-alignment behavior of PNF under shear-dominated flows. Furthermore, we assess the alignment and flow profile of PNF at both high and low flow rates. The length of PNF emerges as a controlling parameter capable of modulating PNF alignment at specific shear rates. Our results shed new insights into the hydrodynamic behavior of PNF, which is highly relevant to various industrial processes involving the fibril systems.
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Affiliation(s)
- Tatiana P Santos
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
| | - Vincenzo Calabrese
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | | | - Stefan K Baier
- Motif FoodWorks, Inc., Boston, MA, USA; The University of Queensland School of Chemical Engineering, St. Lucia, Queensland, Australia
| | - Amy Q Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
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19
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Rajaratnam S, Soman AP, Phalguna KS, Pradhan SS, Manjunath M, Rao RK, Dandamudi RB, Bhagavatham SKS, Pulukool SK, Rathnakumar S, Kocherlakota S, Pargaonkar A, Veeranna RP, Arumugam N, Almansour AI, Choudhary B, Sivaramakrishnan V. Integrated Omic Analysis Delineates Pathways Modulating Toxic TDP-43 Protein Aggregates in Amyotrophic Lateral Sclerosis. Cells 2023; 12:cells12091228. [PMID: 37174628 PMCID: PMC10177613 DOI: 10.3390/cells12091228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a multi-systemic, incurable, amyloid disease affecting the motor neurons, resulting in the death of patients. The disease is either sporadic or familial with SOD1, C9orf72, FUS, and TDP-43 constituting the majority of familial ALS. Multi-omics studies on patients and model systems like mice and yeast have helped in understanding the association of various signaling and metabolic pathways with the disease. The yeast model system has played a pivotal role in elucidating the gene amyloid interactions. We carried out an integrated transcriptomic and metabolomic analysis of the TDP-43 expressing yeast model to elucidate deregulated pathways associated with the disease. The analysis shows the deregulation of the TCA cycle, single carbon metabolism, glutathione metabolism, and fatty acid metabolism. Transcriptomic analysis of GEO datasets of TDP-43 expressing motor neurons from mice models of ALS and ALS patients shows considerable overlap with experimental results. Furthermore, a yeast model was used to validate the obtained results using metabolite addition and gene knock-out experiments. Taken together, our result shows a potential role for the TCA cycle, cellular redox pathway, NAD metabolism, and fatty acid metabolism in disease. Supplementation of reduced glutathione, nicotinate, and the keto diet might help to manage the disease.
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Affiliation(s)
- Saiswaroop Rajaratnam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Akhil P Soman
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
- Central Water and Power Research Station, Khadakwasla, Pune 411024, Maharashtra, India
| | - Kanikaram Sai Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India
| | - Raksha Kanthavara Rao
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India
| | | | - Sai Krishna Srimadh Bhagavatham
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sujith Kumar Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sriram Rathnakumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
| | - Sai Kocherlakota
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru 560066, Karnataka, India
| | - Ravindra P Veeranna
- Department of Biochemistry, Council of Scientific & Industrial Research (CSIR)-Central Food Technological Research Institute (CFTRI), Mysuru 570020, Karnataka, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, Karnataka, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur 515134, Andhra Pradesh, India
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20
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Kaur C, Kaur V, Rai S, Sharma M, Sen T. Selective recognition of the amyloid marker single thioflavin T using DNA origami-based gold nanobipyramid nanoantennas. NANOSCALE 2023; 15:6170-6178. [PMID: 36917482 DOI: 10.1039/d2nr06389a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The development of effective methods for the detection of protein misfolding is highly beneficial for early stage medical diagnosis and the prevention of many neurodegenerative diseases. Self-assembled plasmonic nanoantennas with precisely tunable nanogaps show extraordinary electromagnetic enhancement, generating extreme signal amplification imperative for the design of ultrasensitive biosensors for point of care applications. Herein, we report the custom arrangement of Au nanobipyramid (Au NBP) monomer and dimer nanoantennas engineered precisely based on the DNA origami technique. Furthermore, we demonstrate the SERS based detection of thioflavin T (ThT), a well-established marker for the detection of amyloid fibril formation, where G-Quadruplexes govern the site-specific attachment of ThT in the plasmonic hotspot. This is the first study for the SERS based detection of the ThT dye attached specifically using a G-Quadruplex complex. The spectroscopic signals of ThT were greatly enhanced due to the designed nanoantennas demonstrating their potential as superior SERS substrates. This study paves the way for boosting the design of next-generation diagnostic tools for the specific and precise detection of various target disease biomarkers using molecular probes.
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Affiliation(s)
- Charanleen Kaur
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab - 140306, India.
| | - Vishaldeep Kaur
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab - 140306, India.
| | - Shikha Rai
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab - 140306, India.
| | - Mridu Sharma
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab - 140306, India.
| | - Tapasi Sen
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab - 140306, India.
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21
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Hagey DW, El Andaloussi S. The promise and challenges of extracellular vesicles in the diagnosis of neurodegenerative diseases. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:227-241. [PMID: 36803813 DOI: 10.1016/b978-0-323-85555-6.00014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Extracellular vesicles (EVs) have emerged as essential means of intercommunication for all cell types, and their role in CNS physiology is increasingly appreciated. Accumulating evidence has demonstrated that EVs play important roles in neural cell maintenance, plasticity, and growth. However, EVs have also been demonstrated to spread amyloids and inflammation characteristic of neurodegenerative disease. Such dual roles suggest that EVs may be prime candidates for neurodegenerative disease biomarker analysis. This is supported by several intrinsic properties of EVs: Populations can be enriched by capturing surface proteins from their cell of origin, their diverse cargo represent the complex intracellular states of the cells they derive from, and they can pass the blood-brain barrier. Despite this promise, there are important questions outstanding in this young field that will need to be answered before it can fulfill its potential. Namely, overcoming the technical challenges of isolating rare EV populations, the difficulties inherent in detecting neurodegeneration, and the ethical considerations of diagnosing asymptomatic individuals. Although daunting, succeeding to answer these questions has the potential to provide unprecedented insight and improved treatment of neurodegenerative disease in the future.
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Affiliation(s)
- Daniel W Hagey
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
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22
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Li K, Li A, Mei Y, Zhao J, Zhou Q, Li Y, Yang M, Xu Q. Trace elements and Alzheimer dementia in population-based studies: A bibliometric and meta-analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120782. [PMID: 36464120 DOI: 10.1016/j.envpol.2022.120782] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/05/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Alterations in the concentrations of trace elements may play a vital role in Alzheimer dementia progression. However, previous research results are inconsistent, and there is still a lack of review on the relationship between all the studied-trace elements and AD from various perspectives of population-based studies. In this study, we systematically reviewed previous population-based studies and identified the altered trace elements in AD patients. We searched the Web of Science Core Collection, PubMed, and Scopus database, and ultimately included 73 articles. A bibliometric analysis was conducted to explore the evolution of the field from an epidemiological perspective. Bibliometric data such as trace elements, biological materials, detection methods, cognitive tests, co-occurrence and co-citation statistics are all analyzed and presented in a quantitative manner. The 73 included studies analyzed 39 trace elements in total. In a further meta-analysis, standardized mean differences (SMDs) of 13 elements were calculated to evaluate their altered in AD patients, including copper, iron, zinc, selenium, manganese, lead, aluminum, cadmium, chromium, arsenic, mercury, cobalt, and manganese. We identified four trace elements-copper (serum), iron (plasma), zinc (hair), and selenium (plasma)-altered in AD patients, with SMDs of 0.37 (95% confidence interval [CI]: 0.10, 0.65), -0.68 (95% CI: -1.34, -0.02), -0.35 (95% CI: -0.62, -0.08), and -0.61 (95% CI: -0.97, -0.25), respectively. Finally, we formed a database of various trace element levels in AD patients and healthy controls. Our study can help future researchers gain a comprehensive understanding of the advancements in the field, and our results provide comprehensive population-based data for future research.
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Affiliation(s)
- Kai Li
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Ang Li
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Yayuan Mei
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Jiaxin Zhao
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Quan Zhou
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Yanbing Li
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Ming Yang
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
| | - Qun Xu
- Department of Epidemiology and Biostatistics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China; Center of Environmental and Health Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China.
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23
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Kim Y, Li C, Gu C, Tycksen E, Puri A, Pietka TA, Sivapackiam J, Fang Y, Kidd K, Park SJ, Johnson BG, Kmoch S, Duffield JS, Bleyer AJ, Jackrel ME, Urano F, Sharma V, Lindahl M, Chen YM. MANF stimulates autophagy and restores mitochondrial homeostasis to treat toxic proteinopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523171. [PMID: 36711449 PMCID: PMC9882049 DOI: 10.1101/2023.01.10.523171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Misfolded protein aggregates may cause toxic proteinopathy, including autosomal dominant tubulointerstitial kidney disease due to uromodulin mutations (ADTKD- UMOD ), one of the leading hereditary kidney diseases, and Alzheimer’s disease etc. There are no targeted therapies. ADTKD is also a genetic form of renal fibrosis and chronic kidney disease, which affects 500 million people worldwide. For the first time, in our newly generated mouse model recapitulating human ADTKD- UMOD carrying a leading UMOD deletion mutation, we show that autophagy/mitophagy and mitochondrial biogenesis are severely impaired, leading to cGAS- STING activation and tubular injury. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a novel endoplasmic reticulum stress-regulated secreted protein. We provide the first study that inducible tubular overexpression of MANF after the onset of disease stimulates autophagy/mitophagy and clearance of the misfolded UMOD, and promotes mitochondrial biogenesis through p-AMPK enhancement, resulting in protection of kidney function. Conversely, genetic ablation of endogenous MANF upregulated in the mutant mouse and human tubular cells worsens autophagy suppression and kidney fibrosis. Together, we discover MANF as a novel biotherapeutic protein and elucidate previously unknown mechanisms of MANF in regulating organelle homeostasis to treat ADTKD, which may have broad therapeutic application to treat various proteinopathies.
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24
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Koch KC, Tew GN. Functional antibody delivery: Advances in cellular manipulation. Adv Drug Deliv Rev 2023; 192:114586. [PMID: 36280179 DOI: 10.1016/j.addr.2022.114586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 02/03/2023]
Abstract
The current therapeutic antibody market in the U.S. consists of 100 antibody-based products and their market value is expected to explode beyond $300 billion by 2025. These therapies are presently limited to extracellular targets due to the innate inability of antibodies to transverse membranes. To expand the number of accessible therapeutic targets, intracellular antibody delivery is necessary. Many delivery vehicles for antibodies have been used with some promising results, such as nanoparticles and cell penetrating polymers. Despite the success of these delivery platforms using model antibody cargo, there is a surprisingly small number of studies that focus on functional antibody delivery into the cytosol that also measures a cellular response. Antibodies can be designed for essentially unlimited targets, including proteins and DNA, that will ultimately control cell function once delivered inside cells. Advancement in cellular manipulation depends on the application of intracellularly delivering functional antibodies to achieve a desired result. This review focuses on the emerging field of functional antibody delivery which enables various cellular responses and cell manipulation.
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Affiliation(s)
- Kayla C Koch
- Department of Polymer Science & Engineering, University of Massachusetts, Amherst, MA 01003, United States
| | - Gregory N Tew
- Department of Polymer Science & Engineering, University of Massachusetts, Amherst, MA 01003, United States; Molecular & Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, United States; Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003, United States.
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25
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Bagree G, De Silva O, Liyanage PD, Ramarathinam SH, Sharma SK, Bansal V, Ramanathan R. α-synuclein as a potential biomarker for developing diagnostic tools against neurodegenerative disorders. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Meena P, Kishore N. Potential of tetradecyltrimethylammonium bromide in preventing fibrillation/aggregation of lysozyme: biophysical studies. J Biomol Struct Dyn 2022; 40:13378-13391. [PMID: 34662249 DOI: 10.1080/07391102.2021.1987989] [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: 12/29/2022]
Abstract
A key step in the prevention of neurodegenerative disorders is to inhibit protein aggregation or fibrillation process. Functionality recognition is an essential strategy in developing effective therapeutics in addressing the treatment of amyloidosis. Here, we have focused on an approach based on structure-property energetics correlation associated with tetradecyltrimethylammonium bromide (TTAB), a cationic surfactant that acts as an inhibitor targeting different stages of hen egg-white lysozyme fibrillation. Characterization of amyloid fibrils and the inhibitory capability of 16 mM TTAB surfactant on fibrillation were investigated with the calorimetric, spectroscopic and microscopic techniques. ThT binding fluorescence studies inferred that micellar TTAB exerts its maximum inhibitory effect against amyloid fibrillation than monomer TTAB. The TEM measurements also confirmed complete absence of amyloid fibrils at micellar TTAB. At the same time, the transformation of β-sheet to α-helix under the action of TTAB was confirmed by the Far-UV CD spectroscopy. Although there have been some reports suggesting that cationic surfactants can induce aggregation in proteins, this work suggests that polar interactions between head groups of TTAB and amyloid fibrils are the predominant factors that cause retardation in fibrillation by interrupting/disturbing the intermolecular hydrogen bond of β-sheets. The present finding has explored the knowledge-based details in developing efficient potent inhibitors and provides a platform to treat diseases associated with protein misfolding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pooja Meena
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
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27
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Banerjee S, Baghel D, Iqbal MHU, Ghosh A. Nanoscale Infrared Spectroscopy Identifies Parallel to Antiparallel β-Sheet Transformation of Aβ Fibrils. J Phys Chem Lett 2022; 13:10522-10526. [PMID: 36342244 PMCID: PMC10079140 DOI: 10.1021/acs.jpclett.2c02998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Spontaneous aggregation of amyloid beta (Aβ) proteins leading to the formation of oligomers and eventually into fibrils has been identified as a key pathological signature of Alzheimer's disease. The structure of late-stage aggregates have been studied in depth by conventional structural biology techniques, including nuclear magnetic resonance, X-ray crystallography, and infrared spectroscopy; however, the structure of early-stage aggregates is less known due to their transient nature. As a result, the structural evolution of amyloid aggregates from early oligomers to mature fibrils is still not fully understood. Here, we have applied atomic force microscopy-infrared nanospectroscopy to investigate the aggregation of Aβ 16-22, which spans the amyloidogenic core of the Aβ peptide. Our results demonstrate that Aβ 16-22 involves a structural transition from oligomers with parallel β-sheets to antiparallel fibrils through disordered and possibly helical intermediate fibril structures, contrary to the known aggregation pathway of full-length Aβ.
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Affiliation(s)
- Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
| | - Divya Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
| | - Md Hasan ul Iqbal
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
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28
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Phase separation and other forms of α-Synuclein self-assemblies. Essays Biochem 2022; 66:987-1000. [DOI: 10.1042/ebc20220055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Abstract
α-Synuclein (α-Syn) is a natively unstructured protein, which self-assembles into higher-order aggregates possessing serious pathophysiological implications. α-Syn aberrantly self-assembles into protein aggregates, which have been widely implicated in Parkinson’s disease (PD) pathogenesis and other synucleinopathies. The self-assembly of α-Syn involves the structural conversion of soluble monomeric protein into oligomeric intermediates and eventually fibrillar aggregates of amyloids with cross-β-sheet rich conformation. These aggregated α-Syn species majorly constitute the intraneuronal inclusions, which is a hallmark of PD neuropathology. Self-assembly/aggregation of α-Syn is not a single-state conversion process as unfolded protein can access multiple conformational states through the formation of metastable, transient pre-fibrillar intermediate species. Recent studies have indicated that soluble oligomers are the potential neurotoxic species responsible for cell death in PD pathogenesis. The heterogeneous and transient nature of oligomers formed during the early stage of aggregation pathway limit their detailed study in understanding the structure–toxicity relationship. Moreover, the precise molecular events occurring in the early stage of α-Syn aggregation process majorly remain unsolved. Recently, liquid–liquid phase separation (LLPS) of α-Syn has been designated as an alternate nucleation mechanism, which occurs in the early lag phase of the aggregation pathway leading to the formation of dynamic supramolecular assemblies. The stronger self-association among the protein molecules triggers the irreversible liquid-to-solid transition of these supramolecular assemblies into the amyloid-like hydrogel, which may serve as a reservoir entrapping toxic oligomeric intermediates and fibrils. This review strives to provide insights into different modes of α-Syn self-assemblies including LLPS-mediated self-assembly and its recent advancements.
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29
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Chiu YJ, Lin TH, Chang KH, Lin W, Hsieh-Li HM, Su MT, Chen CM, Sun YC, Lee-Chen GJ. Novel TRKB agonists activate TRKB and downstream ERK and AKT signaling to protect Aβ-GFP SH-SY5Y cells against Aβ toxicity. Aging (Albany NY) 2022; 14:7568-7586. [PMID: 36170028 PMCID: PMC9550238 DOI: 10.18632/aging.204306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/17/2022] [Indexed: 11/28/2022]
Abstract
Decreased BDNF and impaired TRKB signaling contribute to neurodegeneration in Alzheimer’s disease (AD). We have shown previously that coumarin derivative LM-031 enhanced CREB/BDNF/BCL2 pathway. In this study we explored if LM-031 analogs LMDS-1 to -4 may act as TRKB agonists to protect SH-SY5Y cells against Aβ toxicity. By docking computation for binding with TRKB using 7,8-DHF as a control, all four LMDS compounds displayed potential of binding to domain d5 of TRKB. In addition, all four LMDS compounds exhibited anti-aggregation and neuroprotective efficacy on SH-SY5Y cells with induced Aβ-GFP expression. Knock-down of TRKB significantly attenuated TRKB downstream signaling and the neurite outgrowth-promoting effects of these LMDS compounds. Among them, LMDS-1 and -2 were further examined for TRKB signaling. Treatment of ERK inhibitor U0126 or PI3K inhibitor wortmannin decreased p-CREB, BDNF and BCL2 in Aβ-GFP cells, implicating the neuroprotective effects are via activating TRKB downstream ERK, PI3K-AKT and CREB signaling. LMDS-1 and -2 are blood–brain barrier permeable as shown by parallel artificial membrane permeability assay. Our results demonstrate how LMDS-1 and -2 are likely to work as TRKB agonists to exert neuroprotection in Aβ cells, which may shed light on the potential application in therapeutics of AD.
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Affiliation(s)
- Ya-Jen Chiu
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Te-Hsien Lin
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Kuo-Hsuan Chang
- Department of Neurology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33302, Taiwan
| | - Wenwei Lin
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Hsiu Mei Hsieh-Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Ming-Tsan Su
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Chiung-Mei Chen
- Department of Neurology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan 33302, Taiwan
| | - Ying-Chieh Sun
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Guey-Jen Lee-Chen
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan
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30
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Morzan UN, Díaz Mirón G, Grisanti L, González Lebrero MC, Kaminski Schierle GS, Hassanali A. Non-Aromatic Fluorescence in Biological Matter: The Exception or the Rule? J Phys Chem B 2022; 126:7203-7211. [PMID: 36128666 DOI: 10.1021/acs.jpcb.2c04280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While in the vast majority of cases fluorescence in biological matter has been attributed to aromatic or conjugated groups, peptides associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, or Huntington's, have been recently shown to display an intrinsic visible fluorescence even in the absence of aromatic residues. This has called the attention of researchers from many different fields, trying to understand the origin of this peculiar behavior and, at the same time, motivating the search for novel strategies to control the optical properties of new biophotonic materials. Today, after nearly 15 years of its discovery, there is a growing consensus about the mechanism underlying this phenomenon, namely, that electronic interactions between non-optically active molecules can result in supramolecular assemblies that are fluorescent. Despite this progress, many aspects of this phenomenon remain uncharted territory. In this Perspective, we lay down the state-of-the-art in the field highlighting the open questions from both experimental and theoretical fronts in this fascinating emerging area of non-aromatic fluorescence.
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Affiliation(s)
- Uriel N Morzan
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Gonzalo Díaz Mirón
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | - Luca Grisanti
- Division of Theoretical Physics, Ruđer Bos̆cković Institute, Bijenic̆ka cesta 54, 10000 Zagreb, Croatia
| | - Mariano C González Lebrero
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | | | - Ali Hassanali
- International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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31
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Tripathi R, Gupta R, Sahu M, Srivastava D, Das A, Ambasta RK, Kumar P. Free radical biology in neurological manifestations: mechanisms to therapeutics interventions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62160-62207. [PMID: 34617231 DOI: 10.1007/s11356-021-16693-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Recent advancements and growing attention about free radicals (ROS) and redox signaling enable the scientific fraternity to consider their involvement in the pathophysiology of inflammatory diseases, metabolic disorders, and neurological defects. Free radicals increase the concentration of reactive oxygen and nitrogen species in the biological system through different endogenous sources and thus increased the overall oxidative stress. An increase in oxidative stress causes cell death through different signaling mechanisms such as mitochondrial impairment, cell-cycle arrest, DNA damage response, inflammation, negative regulation of protein, and lipid peroxidation. Thus, an appropriate balance between free radicals and antioxidants becomes crucial to maintain physiological function. Since the 1brain requires high oxygen for its functioning, it is highly vulnerable to free radical generation and enhanced ROS in the brain adversely affects axonal regeneration and synaptic plasticity, which results in neuronal cell death. In addition, increased ROS in the brain alters various signaling pathways such as apoptosis, autophagy, inflammation and microglial activation, DNA damage response, and cell-cycle arrest, leading to memory and learning defects. Mounting evidence suggests the potential involvement of micro-RNAs, circular-RNAs, natural and dietary compounds, synthetic inhibitors, and heat-shock proteins as therapeutic agents to combat neurological diseases. Herein, we explain the mechanism of free radical generation and its role in mitochondrial, protein, and lipid peroxidation biology. Further, we discuss the negative role of free radicals in synaptic plasticity and axonal regeneration through the modulation of various signaling molecules and also in the involvement of free radicals in various neurological diseases and their potential therapeutic approaches. The primary cause of free radical generation is drug overdosing, industrial air pollution, toxic heavy metals, ionizing radiation, smoking, alcohol, pesticides, and ultraviolet radiation. Excessive generation of free radicals inside the cell R1Q1 increases reactive oxygen and nitrogen species, which causes oxidative damage. An increase in oxidative damage alters different cellular pathways and processes such as mitochondrial impairment, DNA damage response, cell cycle arrest, and inflammatory response, leading to pathogenesis and progression of neurodegenerative disease other neurological defects.
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Affiliation(s)
- Rahul Tripathi
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Delhi, India
| | - Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Delhi, India
| | - Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Delhi, India
| | - Devesh Srivastava
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Delhi, India
| | - Ankita Das
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Delhi, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Delhi, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), Delhi, India.
- , Delhi, India.
- Molecular Neuroscience and Functional Genomics Laboratory, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
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32
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Hormozi Jangi SR, Akhond M. Introducing a covalent thiol-based protected immobilized acetylcholinesterase with enhanced enzymatic performances for biosynthesis of esters. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Housmans JAJ, Houben B, Monge-Morera M, Asvestas D, Nguyen HH, Tsaka G, Louros N, Carpentier S, Delcour JA, Rousseau F, Schymkowitz J. Investigating the Sequence Determinants of the Curling of Amyloid Fibrils Using Ovalbumin as a Case Study. Biomacromolecules 2022; 23:3779-3797. [PMID: 36027608 DOI: 10.1021/acs.biomac.2c00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Highly ordered, straight amyloid fibrils readily lend themselves to structure determination techniques and have therefore been extensively characterized. However, the less ordered curly fibrils remain relatively understudied, and the structural organization underlying their specific characteristics remains poorly understood. We found that the exemplary curly fibril-forming protein ovalbumin contains multiple aggregation prone regions (APRs) that form straight fibrils when isolated as peptides or when excised from the full-length protein through hydrolysis. In the context of the intact full-length protein, however, the regions separating the APRs facilitate curly fibril formation. In fact, a meta-analysis of previously reported curly fibril-forming proteins shows that their inter-APRs are significantly longer and more hydrophobic when compared to straight fibril-forming proteins, suggesting that they may cause strain in the amyloid state. Hence, inter-APRs driving curly fibril formation may not only apply to our model protein but rather constitute a more general mechanism.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Margarita Monge-Morera
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Diego Asvestas
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Hung Huy Nguyen
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Grigoria Tsaka
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Sebastien Carpentier
- Facility for Systems Biology Based Mass Spectrometry, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jan A Delcour
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
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34
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Sen A, Mora AK, Koli M, Mula S, Kundu S, Nath S. Sensing lysozyme fibrils by salicylaldimine substituted BODIPY dyes - A correlation with molecular structure. Int J Biol Macromol 2022; 220:901-909. [PMID: 35998856 DOI: 10.1016/j.ijbiomac.2022.08.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022]
Abstract
Quick and efficient detection of protein fibrils has enormous impact on the diagnosis and treatment of amyloid related neurological diseases. Among several methods, fluorescence based techniques have garnered most importance in the detection of amyloid fibrils due to its high sensitivity and extreme simplicity. Among other classes of molecular probes, BODIPY derivatives have been employed extensively for the detection of amyloid fibrils. However, there are very few studies on the relationship between the molecular structure of BODIPY dyes and their amyloid sensing activity. Here in a BODIPY based salicylaldimine Schiff base and its corresponding boron complex have been evaluated for their ability to sense amyloid fibrils from hen-egg white lysozyme using steady state and time-resolved spectroscopic techniques. Both dyes show fluorescence enhancement as well as increase in their excited state lifetime upon their binding with lysozyme fibrils. However, the BODIPY derivative which shows more emission enhancement in fibrillar solution has much lower affinity towards amyloid fibrils as compared to other derivative. This contrasting behaviour in the emission enhancement and binding affinity has been explained on the basis of differences in their photophysical properties in water and amyloid fibril originating from the difference in their molecular structure. Such correlation between the amyloid sensitivity and the molecular structure of the probe can open up a new strategy for designing new efficient amyloid probes.
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Affiliation(s)
- Ayentika Sen
- Beam Technology Development Group, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Aruna K Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India.
| | - Mrunesh Koli
- Bio-Organic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Soumyaditya Mula
- Bio-Organic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India
| | - Soumitra Kundu
- Beam Technology Development Group, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400 094, India.
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Pillai VS, Kumari P, Kolagatla S, Garcia Sakai V, Rudić S, Rodriguez BJ, Rubini M, Tych KM, Benedetto A. Controlling Amyloid Fibril Properties Via Ionic Liquids: The Representative Case of Ethylammonium Nitrate and Tetramethylguanidinium Acetate on the Amyloidogenesis of Lysozyme. J Phys Chem Lett 2022; 13:7058-7064. [PMID: 35900133 PMCID: PMC9358703 DOI: 10.1021/acs.jpclett.2c01505] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein aggregation into amyloid fibrils has been observed in several pathological conditions and exploited in nanotechnology. It is also key in several biochemical processes. In this work, we show that ionic liquids (ILs), a vast class of organic electrolytes, can finely tune amyloid properties, opening a new landscape in basic science and applications. The representative case of ethylammonium nitrate (EAN) and tetramethyl-guanidinium acetate (TMGA) ILs on lysozyme is considered. First, atomic force microscopy has shown that the addition of EAN and TMGA leads to thicker and thinner amyloid fibrils of greater and lower electric potential, respectively, with diameters finely tunable by IL concentration. Optical tweezers and neutron scattering have shed light on their mechanism of action. TMGA interacts with the protein hydration layer only, making the relaxation dynamics of these water molecules faster. EAN interacts directly with the protein instead, making it mechanically unstable and slowing down its relaxation dynamics.
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Affiliation(s)
- Visakh
V. S. Pillai
- School
of Physics, University College Dublin, Dublin D04 N2E5, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 N2E5, Ireland
| | - Pallavi Kumari
- School
of Physics, University College Dublin, Dublin D04 N2E5, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 N2E5, Ireland
| | - Srikanth Kolagatla
- School
of Physics, University College Dublin, Dublin D04 N2E5, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 N2E5, Ireland
| | - Victoria Garcia Sakai
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, U.K.
| | - Svemir Rudić
- ISIS
Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, U.K.
| | - Brian J. Rodriguez
- School
of Physics, University College Dublin, Dublin D04 N2E5, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 N2E5, Ireland
| | - Marina Rubini
- School
of Chemistry, University College Dublin, Dublin D04 N2E5, Ireland
| | - Katarzyna M. Tych
- Groningen
Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Antonio Benedetto
- School
of Physics, University College Dublin, Dublin D04 N2E5, Ireland
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 N2E5, Ireland
- Department
of Science, University of Roma Tre, 00146 Rome, Italy
- Laboratory
for Neutron Scattering, Paul Scherrer Institute, 5232 Villigen, Switzerland
- , ,
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Navalkar A, Paul A, Sakunthala A, Pandey S, Dey AK, Saha S, Sahoo S, Jolly MK, Maiti TK, Maji SK. Oncogenic gain of function due to p53 amyloids by aberrant alteration of cell cycle and proliferation. J Cell Sci 2022; 135:276165. [PMID: 35796018 DOI: 10.1242/jcs.259500] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/04/2022] [Indexed: 11/20/2022] Open
Abstract
Transcription factor p53 has been shown to aggregate into cytoplasmic/nuclear inclusions, compromising its native tumor suppressive functions. Recently, p53 is shown to form amyloids, which play a role in conferring cancerous properties to cells leading to tumorigenesis. However, the exact pathways involved in p53 amyloid-mediated cellular transformations are unknown. Here, using an in cellulo model of full-length p53 amyloid formation, we demonstrate the mechanism of loss of p53 tumor-suppressive function with concomitant oncogenic gain-of functions. Global gene expression profiling of cells suggests that p53 amyloid formation dysregulates the genes associated with cell cycle, proliferation, apoptosis, senescence along with major signaling pathways. This is further supported by the proteome analysis, showing a significant alteration in levels of p53 target proteins and enhanced metabolism, which enables the survival of cells. Our data indicate that specifically targeting the key molecules in pathways affected by p53 amyloid formation such as cyclin-dependent kinase-1, leads to loss of oncogenic phenotype and induces apoptosis of cells. Overall, our work establishes the mechanism of the transformation of cells due to p53 amyloids leading to cancer pathogenesis.
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Affiliation(s)
- Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Ajoy Paul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Arunima Sakunthala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Satyaprakash Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Amit Kumar Dey
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Sandhini Saha
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bengaluru 560012, India
| | - Mohit K Jolly
- Centre for BioSystems Science and Engineering (BSSE), Indian Institute of Science, Bengaluru 560012, India
| | - Tushar K Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
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New Insights into the Multivariate Analysis of SER Spectra Collected on Blood Samples for Prostate Cancer Detection: Towards a Better Understanding of the Role Played by Different Biomolecules on Cancer Screening: A Preliminary Study. Cancers (Basel) 2022; 14:cancers14133227. [PMID: 35804993 PMCID: PMC9264810 DOI: 10.3390/cancers14133227] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary In recent years, research on biofluids using Raman and SERS has expanded dramatically, indicating the enormous promise of this technology as a high-throughput tool for identifying cancer and other disorders. In the investigations thus far, researchers have concentrated on a specific illness or condition, but the techniques employed to acquire experimental spectra prevent direct comparison of the data. This necessitates comparative research of a variety of diseases and an increase in scientific cooperation to standardize experimental conditions. In our study, positive results were reached by applying a combined SERS multivariate analysis (MVA) to the urgent problem of prostate cancer diagnosis that was directly linked to real-world settings in healthcare. Moreover, in comparison to the prostate-specific antigen (PSA) test, which has a high sensitivity but limited specificity, our combined SERS-MVA method has greater specificity, which may assist in preventing the overtreatment of patients. Abstract It is possible to obtain diagnostically relevant data on the changes in biochemical elements brought on by cancer via the use of multivariate analysis of vibrational spectra recorded on biological fluids. Prostate cancer and control groups included in this research generated almost similar SERS spectra, which means that the values of peak intensities present in SERS spectra can only give unspecific and limited information for distinguishing between the two groups. Our diagnostic algorithm for prostate cancer (PCa) differentiation was built using principal component analysis and linear discriminant analysis (PCA-LDA) analysis of spectral data, which has been widely used in spectral data management in many studies and has shown promising results so far. In order to fully utilize the entire SERS spectrum and automatically determine the most meaningful spectral features that can be used to differentiate PCa from healthy patients, we perform a multivariate analysis on both the entire and specific spectral intervals. Using the PCA-LDA model, the prostate cancer and control groups are clearly distinguished in our investigation. The separability of the following two data sets is also evaluated using two alternative discrimination techniques: principal least squares discriminant analysis (PLS-DA) and principal component analysis—support vector machine (PCA-SVM).
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Behera A, Sharma O, Paul D, Sain A. Temperature-dependent Self assembly of biofilaments during red blood cell sickling. J Chem Phys 2022; 157:014105. [DOI: 10.1063/5.0091690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular self-assembly plays vital role in various biological functions. However, when aberrant molecules self-assemble to form large aggregates, it can give rise to various diseases. For example, the sickle cell disease andAlzheimer's disease are caused by self-assembled hemoglobin fibers and amyloid plaques, respectively. Here we studythe assembly kinetics of such fibers using kinetic Monte- Carlo simulation. We focus on the initial lag time of thesehighly stochastic processes, during which self-assembly is very slow. The lag time distributions turn out to be similarfor two very different regimes of polymerization, namely, a) when polymerization is slow and depolymerization is fast,and b) the opposite case, when polymerization is fast and depolymerization is slow. Using temperature dependent on-and off-rates for hemoglobin fiber growth, reported in recent in-vitro experiments, we show that the mean lag time canexhibit non-monotonic behavior with respect to change in temperature.
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Affiliation(s)
| | - Oshin Sharma
- Indian Institute of Technology Bombay Department of Biosciences and Bioengineering, India
| | - Debjani Paul
- Biosciences and Bioengineering, Indian Institute of Technology Bombay, India
| | - Anirban Sain
- Physics, Indian Institute of Technology Bombay Department of Physics, India
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Fanni AM, Okoye D, Monge FA, Hammond J, Maghsoodi F, Martin TD, Brinkley G, Phipps ML, Evans DG, Martinez JS, Whitten DG, Chi EY. Controlled and Selective Photo-oxidation of Amyloid-β Fibrils by Oligomeric p-Phenylene Ethynylenes. ACS APPLIED MATERIALS & INTERFACES 2022; 14:14871-14886. [PMID: 35344326 PMCID: PMC10452927 DOI: 10.1021/acsami.1c22869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Photodynamic therapy (PDT) has been explored as a therapeutic strategy to clear toxic amyloid aggregates involved in neurodegenerative disorders such as Alzheimer's disease. A major limitation of PDT is off-target oxidation, which can be lethal for the surrounding cells. We have shown that a novel class of oligo-p-phenylene ethynylenes (OPEs) exhibit selective binding and fluorescence turn-on in the presence of prefibrillar and fibrillar aggregates of disease-relevant proteins such as amyloid-β (Aβ) and α-synuclein. Concomitant with fluorescence turn-on, OPE also photosensitizes singlet oxygen under illumination through the generation of a triplet state, pointing to the potential application of OPEs as photosensitizers in PDT. Herein, we investigated the photosensitizing activity of an anionic OPE for the photo-oxidation of Aβ fibrils and compared its efficacy to the well-known but nonselective photosensitizer methylene blue (MB). Our results show that, while MB photo-oxidized both monomeric and fibrillar conformers of Aβ40, OPE oxidized only Aβ40 fibrils, targeting two histidine residues on the fibril surface and a methionine residue located in the fibril core. Oxidized fibrils were shorter and more dispersed but retained the characteristic β-sheet rich fibrillar structure and the ability to seed further fibril growth. Importantly, the oxidized fibrils displayed low toxicity. We have thus discovered a class of novel theranostics for the simultaneous detection and oxidization of amyloid aggregates. Importantly, the selectivity of OPE's photosensitizing activity overcomes the limitation of off-target oxidation of traditional photosensitizers and represents an advancement of PDT as a viable strategy to treat neurodegenerative disorders.
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Affiliation(s)
- Adeline M. Fanni
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131
- Biomedical Engineering Graduate Program, University of New Mexico, Albuquerque, NM. 87131
| | - Daniel Okoye
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Florencia A. Monge
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131
- Biomedical Engineering Graduate Program, University of New Mexico, Albuquerque, NM. 87131
| | - Julia Hammond
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM. 87131
- Rose-Hulman Institute of Technology, Terre Haute, IN 47803
| | - Fahimeh Maghsoodi
- Nanoscience and Microsystems Engineering Graduate Program, University of New Mexico, Albuquerque, NM 87131
| | - Tye D. Martin
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131
- Biomedical Engineering Graduate Program, University of New Mexico, Albuquerque, NM. 87131
| | - Gabriella Brinkley
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM. 87131
- Chemical Engineering Department, University of Minnesota, Duluth, MN 55812
| | - M. Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Deborah G. Evans
- Department of Chemistry and Chemical Biology, University of New Mexico, NM 87131
| | - Jennifer S. Martinez
- Center for Materials Interfaces in Research and Applications, Northern Arizona University, Flagstaff, AZ 86011
- Department of Applied Physics and Materials Science, Northern Arizona University, Flagstaff, AZ 86011
| | - David G. Whitten
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM. 87131
| | - Eva Y. Chi
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, NM 87131
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM. 87131
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40
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Picornavirus May Be Linked to Parkinson’s Disease through Viral Antigen in Dopamine-Containing Neurons of Substantia Nigra. Microorganisms 2022; 10:microorganisms10030599. [PMID: 35336174 PMCID: PMC8953350 DOI: 10.3390/microorganisms10030599] [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: 01/10/2022] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 11/17/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disease linked with the loss of dopaminergic neurons in the brain region called substantia nigra and caused by unknown pathogenic mechanisms. Two currently recognized prominent features of PD are an inflammatory response manifested by glial reaction and T-cell infiltration, as well as the presence of various toxic mediators derived from activated glial cells. PD or parkinsonism has been described after infection with several different viruses and it has therefore been hypothesized that a viral infection might play a role in the pathogenesis of the disease. We investigated formalin-fixed post-mortem brain tissue from 9 patients with Parkinson’s disease and 11 controls for the presence of Ljungan virus (LV) antigen using a polyclonal antibody against the capsid protein of this recently identified picornavirus with neurotropic properties, suspected of being both a human and an animal pathogen. Evidence of viral antigen was found in 7 out of 9 Parkinson’s disease cases and in only 1 out of 11 controls (p = 0.005). The picornavirus antigen was present in dopamine-containing neurons of the substantia nigra. We propose that LV or an LV-related virus initiates the pathological process underlying sporadic PD. LV-related picornavirus antigen has also been reported in patients with Alzheimer’s disease. Potentially successful antiviral treatment in Alzheimer’s disease suggests a similar treatment for Parkinson's disease. Amantadine, originally developed as an antiviral drug against influenza infection, has also been used for symptomatic treatment of patients with PD for more than 50 years and is still commonly used by neurologists today. The fact that amantadine also has an antiviral effect on picornaviruses opens the question of this drug being re-evaluated as potential PD therapy in combination with other antiviral compounds directed against picornaviruses.
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41
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van Gils JHM, Gogishvili D, van Eck J, Bouwmeester R, van Dijk E, Abeln S. How sticky are our proteins? Quantifying hydrophobicity of the human proteome. BIOINFORMATICS ADVANCES 2022; 2:vbac002. [PMID: 36699344 PMCID: PMC9710682 DOI: 10.1093/bioadv/vbac002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/19/2021] [Accepted: 01/24/2022] [Indexed: 01/28/2023]
Abstract
Summary Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the solvent. These residues can play an important functional role, e.g. in protein-protein and membrane interactions. Here, we first investigate how hydrophobic protein surfaces are by providing three measures for surface hydrophobicity: the total hydrophobic surface area, the relative hydrophobic surface area and-using our MolPatch method-the largest hydrophobic patch. Secondly, we analyze how difficult it is to predict these measures from sequence: by adapting solvent accessibility predictions from NetSurfP2.0, we obtain well-performing prediction methods for the THSA and RHSA, while predicting LHP is more challenging. Finally, we analyze implications of exposed hydrophobic surfaces: we show that hydrophobic proteins typically have low expression, suggesting cells avoid an overabundance of sticky proteins. Availability and implementation The data underlying this article are available in GitHub at https://github.com/ibivu/hydrophobic_patches. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Juami Hermine Mariama van Gils
- Computer Science Department, Center for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Noord-Holland, The Netherlands,To whom correspondence should be addressed. or
| | - Dea Gogishvili
- Computer Science Department, Center for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Noord-Holland, The Netherlands
| | - Jan van Eck
- Computer Science Department, Center for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Noord-Holland, The Netherlands
| | - Robbin Bouwmeester
- Computer Science Department, Center for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Noord-Holland, The Netherlands
| | - Erik van Dijk
- Computer Science Department, Center for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Noord-Holland, The Netherlands
| | - Sanne Abeln
- Computer Science Department, Center for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Noord-Holland, The Netherlands,To whom correspondence should be addressed. or
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42
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Ge P, Yang M, Bouchard JL, Dzamko N, Lewis SJG, Halliday GM, Doran TM. Chemoselective Bioconjugation of Amyloidogenic Protein Antigens to PEGylated Microspheres Enables Detection of α-Synuclein Autoantibodies in Human Plasma. Bioconjug Chem 2022; 33:301-310. [PMID: 35020392 DOI: 10.1021/acs.bioconjchem.1c00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The misfolding and subsequent aggregation of amyloidogenic proteins is a classic pathological hallmark of neurodegenerative diseases. Aggregates of the α-synuclein protein (αS) are implicated in Parkinson's disease (PD) pathogenesis, and naturally occurring autoantibodies to these aggregates are proposed to be potential early-stage biomarkers to facilitate the diagnosis of PD. However, upon misfolding, αS forms a multitude of quaternary structures of varying functions that are unstable ex vivo. Thus, when used as a capture agent in enzyme-linked immunosorbent assays (ELISAs), significant variance among laboratories has prevented the development of these valuable diagnostic tests. We reasoned that those conflicting results arise due to the high nonspecific binding and amyloid nucleation that are typical of ELISA platforms. In this work, we describe a multiplexed, easy-to-operate immunoassay that is generally applicable to quantify the levels of amyloid proteins and their binding partners, named Oxaziridine-Assisted Solid-phase Immunosorbent (OASIS) assay. The assay is built on a hydrophilic poly(ethylene glycol) scaffold that inhibits aggregate nucleation, which we show reduces assay variance when compared to similar ELISA measurements. To validate our OASIS assay in patient-derived samples, we measured the levels of naturally occurring antibodies against the αS monomer and oligomers in a cohort of donor plasma from patients diagnosed with PD. Using OASIS assays, we observed significantly higher titers of immunoglobulin G antibody recognizing αS oligomers in PD patients compared to those in healthy controls, while there was no significant difference in naturally occurring antibodies against the αS monomer. In addition to its development into a blood test to potentially predict or monitor PD, we anticipate that the OASIS assay will be of high utility for studies aimed at understanding protein misfolding, its pathology and symptomology in PD, and other neurodegenerative diseases.
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Affiliation(s)
- Peng Ge
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mu Yang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jacob L Bouchard
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Nicolas Dzamko
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Simon J G Lewis
- Parkinson's Disease Research Clinic, Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Glenda M Halliday
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Todd M Doran
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Shahbaz SK, Koushki K, Sathyapalan T, Majeed M, Sahebkar A. PLGA-Based Curcumin Delivery System: An Interesting Therapeutic Approach in the Treatment of Alzheimer's Disease. Curr Neuropharmacol 2022; 20:309-323. [PMID: 34429054 PMCID: PMC9413791 DOI: 10.2174/1570159x19666210823103020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/23/2021] [Accepted: 07/24/2021] [Indexed: 11/22/2022] Open
Abstract
Progressive degeneration and dysfunction of the nervous system because of oxidative stress, aggregations of misfolded proteins, and neuroinflammation are the key pathological features of neurodegenerative diseases. Alzheimer's disease is a chronic neurodegenerative disorder driven by uncontrolled extracellular deposition of β-amyloid (Aβ) in the amyloid plaques and intracellular accumulation of hyperphosphorylated tau protein. Curcumin is a hydrophobic polyphenol with noticeable neuroprotective and anti-inflammatory effects that can cross the blood-brain barrier. Therefore, it is widely studied for the alleviation of inflammatory and neurological disorders. However, the clinical application of curcumin is limited due to its low aqueous solubility and bioavailability. Recently, nano-based curcumin delivery systems are developed to overcome these limitations effectively. This review article discusses the effects and potential mechanisms of curcumin-loaded PLGA nanoparticles in Alzheimer's disease.
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Affiliation(s)
- Sanaz Keshavarz Shahbaz
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Khadijeh Koushki
- Hepatitis Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Thozhukat Sathyapalan
- Department of Academic Diabetes, Endocrinology and Metabolism, Hull York Medical School, University of Hull, Hull HU3 2JZ, UK
| | | | - Amirhossein Sahebkar
- BARUiotechnol Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Medicine, The University of Western Australia, Perth, Australia
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Fontana NA, Rosse AD, Watts A, Coelho PSR, Costa-Filho AJ. In vivo observation of amyloid-like fibrils produced under stress. Int J Biol Macromol 2021; 199:42-50. [PMID: 34942208 DOI: 10.1016/j.ijbiomac.2021.12.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
The participation of amyloids in neurodegenerative diseases and functional processes has triggered the quest for methods allowing their direct detection in vivo. Despite the plethora of data, those methods are still lacking. The autofluorescence from the extended β-sheets of amyloids is here used to follow fibrillation of S. cerevisiae Golgi Reassembly and Stacking Protein (Grh1). Grh1 has been implicated in starvation-triggered unconventional protein secretion (UPS), and here its participation also in heat shock response (HSR) is suggested. Fluorescence Lifetime Imaging (FLIM) is used to detect fibril autofluorescence in cells (E. coli and yeast) under stress (starvation and higher temperature). The formation of Grh1 large complexes under stress is further supported by size exclusion chromatography and ultracentrifugation. The data show for the first time in vivo detection of amyloids without the use of extrinsic probes as well as bring new perspectives on the participation of Grh1 in UPS and HSR.
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Affiliation(s)
- Natália A Fontana
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Ariane D Rosse
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Paulo S R Coelho
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Antonio J Costa-Filho
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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45
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Impact of Synthesized AuNPs from Crocin Against Aggregation and Conformational Change in α-Lactalbumin. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10252-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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46
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Jiang B, Martí AA. Probing Amyloid Nanostructures Using Photoluminescent Metal Complexes. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
Affiliation(s)
- Bo Jiang
- Department of Chemistry Rice University 6100 Main St, Chemistry MS60 Houston Texas 77005 United States
| | - Angel A. Martí
- Department of Chemistry Department of Bioengineering, and Department of Material Science & NanoEngineering Rice University 6100 Main St, Chemistry MS60 Houston Texas 77005 United States
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Foley AR, Raskatov JA. Understanding and controlling amyloid aggregation with chirality. Curr Opin Chem Biol 2021; 64:1-9. [PMID: 33610939 PMCID: PMC8368077 DOI: 10.1016/j.cbpa.2021.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 12/22/2022]
Abstract
Amyloid aggregation and human disease are inextricably linked. Examples include Alzheimer disease, Parkinson disease, and type II diabetes. While seminal advances on the mechanistic understanding of these diseases have been made over the last decades, controlling amyloid fibril formation still represents a challenge, and it is a subject of active research. In this regard, chiral modifications have increasingly been proved to offer a particularly well-suited approach toward accessing to previously unknown aggregation pathways and to provide with novel insights on the biological mechanisms of action of amyloidogenic peptides and proteins. Here, we summarize recent advances on how the use of mirror-image peptides/proteins and d-amino acid incorporations have helped modulate amyloid aggregation, offered new mechanistic tools to study cellular interactions, and allowed us to identify key positions within the peptide/protein sequence that influence amyloid fibril growth and toxicity.
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Affiliation(s)
- Alejandro R Foley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
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Nickel oxide nanoparticles increase α-synuclein amyloid formation and relevant overexpression of inflammatory mediators in microglia as a marker of Parkinson's disease. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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Wang W, Zhao X, Shao Y, Duan X, Wang Y, Li J, Li J, Li D, Li X, Wong J. Mutation-induced DNMT1 cleavage drives neurodegenerative disease. SCIENCE ADVANCES 2021; 7:eabe8511. [PMID: 34516921 PMCID: PMC8442919 DOI: 10.1126/sciadv.abe8511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Specific mutations within the replication foci targeting sequence (RFTS) domain of human DNMT1 are causative of two types of adult-onset neurodegenerative diseases, HSAN1E and ADCA-DN, but the underlying mechanisms are largely unknown. We generated Dnmt1-M1 and Dnmt1-M2 knock-in mouse models that are equivalent to Y495C and D490E-P491Y mutation in patients with HSAN1E, respectively. We found that both mutant heterozygous mice are viable, have reduced DNMT1 proteins, and exhibit neurodegenerative phenotypes including impaired learning and memory. The homozygous mutants die around embryonic day 10.5 and are apparently devoid of DNMT1 proteins. We present the evidence that the mutant DNMT1 proteins are unstable, most likely because of cleavage within RFTS domain by an unidentified proteinase. Moreover, we provide evidence that the RFTS mutation–induced cleavage of DNMT1, but not mutation itself, is responsible for functional defect of mutant DNMT1. Our study shed light on the mechanism of DNMT1 RFTS mutation causing neurodegenerative diseases.
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Affiliation(s)
- Wencai Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
| | - Xingsen Zhao
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
- National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Yanjiao Shao
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiaoya Duan
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yaling Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xuekun Li
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
- National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
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