1
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Imaura R, Kawata Y, Matsuo K. Salt-Induced Hydrophobic C-Terminal Region of α-Synuclein Triggers Its Fibrillation under the Mimic Physiologic Condition. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:20537-20549. [PMID: 39285698 DOI: 10.1021/acs.langmuir.4c02178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
α-Synuclein (αS) causes Parkinson's disease due to the structural alteration into amyloid fibrils that form after the interaction with synaptic membranes in neurons. To understand the alternation mechanism, the effect of salt (NaCl) on the interaction of αS with synaptic mimic membrane was characterized at the molecular level because salt triggered the amyloid fibril formation. The membrane-bound conformation (or the initial conformation before fibrillation) showed that NaCl decreased the number of helical structures and Tyr residues interacting with the membrane surface compared to when NaCl was absent, implying an increase in solvent-exposed regions. The N-terminal region of αS interacted with the membrane, forming the helical structures regardless of NaCl, while the C-terminal region formed a random structure with weak membrane interaction, but NaCl inhibited the interaction of its hydrophobic area, suggesting that salt promoted amyloid fibril formations by exposing the hydrophobic C-terminal region, which can intermolecularly interact with free αS.
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Affiliation(s)
- Ryota Imaura
- Graduate School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8511, Japan
| | - Yasushi Kawata
- Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Koichi Matsuo
- Graduate School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8511, Japan
- Research Institute for Synchrotron Radiation Science, Hiroshima University, Hiroshima 739-0046, Japan
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, Hiroshima 739-0046, Japan
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2
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Devi M, Paul S. Comprehending the Efficacy of Whitlock's Caffeine-Pincered Molecular Tweezer on β-Amyloid Aggregation. ACS Chem Neurosci 2024; 15:3202-3219. [PMID: 39126645 DOI: 10.1021/acschemneuro.4c00387] [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: 08/12/2024] Open
Abstract
Alzheimer's disease (AD) stands as one of the most prevalent neurodegenerative conditions, leading to cognitive impairment, with no cure and preventive measures. Misfolding and aberrant aggregation of amyloid-β (Aβ) peptides are believed to be the underlying cause of AD. These amyloid aggregates culminate in the development of toxic Aβ oligomers and subsequent accumulation of β-amyloid plaques amidst neuronal cells in the brain, marking the hallmarks of AD. Drug development for the potentially curative treatment of Alzheimer's is, therefore, a tremendous challenge for the scientific community. In this study, we investigate the potency of Whitlock's caffeine-armed molecular tweezer in combating the deleterious effects of Aβ aggregation, with special emphasis on the seven residue Aβ16-22 fragment. Extensive all-atom molecular dynamics simulations are conducted to probe the various structural and conformational transitions of the peptides in an aqueous medium in both the presence and absence of tweezers. To explore the specifics of peptide-tweezer interactions, radial distribution functions, contact number calculations, binding free energies, and 2-D kernel density plots depicting the variation of distance-angle between the aromatic planes of the peptide-tweezer pair are computed. The central hydrophobic core, particularly the aromatic Phe residues, is crucial in the development of harmful amyloid oligomers. Notably, all analyses indicate reduced interpeptide interactions in the presence of the tweezer, which is attributed to the tweezer-Phe aromatic interaction. Upon increasing the tweezer concentration, the residues of the peptide are further encased in a hydrophobic environment created by the self-aggregating tweezer cluster, leading to the segregation of the peptide residues. This is further aided by the weakening of interstrand hydrogen bonding between the peptides, thereby impeding their self-aggregation and preventing the formation of neurotoxic β-amyloid. Furthermore, the study also highlights the efficacy of the molecular tweezer in destabilizing preformed amyloid fibrils as well as hindering the aggregation of the full-length Aβ1-42 peptide.
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Affiliation(s)
- Madhusmita Devi
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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3
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Puello-Silva J, Alí-Torres J. Computational 3D Models of Fe 2+/3+-Aβ 1-42 Complexes Associated with Alzheimer's Disease. J Phys Chem B 2024; 128:7022-7032. [PMID: 39016210 DOI: 10.1021/acs.jpcb.4c01173] [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: 07/18/2024]
Abstract
The interaction between iron and amyloid-beta (Aβ) peptides has received significant attention in Alzheimer's disease (AD) research due to its potential implications in developing this pathology. However, the coordination preferences of iron and Aβ1-42 have not been thoroughly investigated or remain unknown. This study employs a computational protocol that combines homology modeling techniques with quantum mechanics (DTF-xTB) calculations to build and evaluate several 3D models of Fe2+/3+-Aβ1-42. Our results reveal well-defined complexes for both the metal and peptide moieties, and we discuss the molecular interactions stabilizing these complexes by elucidating the coordinating environments and binding preferences. These proposed models offer valuable insights into the role of iron in Alzheimer's disease (AD) pathology.
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Affiliation(s)
- Jorge Puello-Silva
- Departamento de Química, Universidad Nacional de Colombia - Sede Bogotá, Bogotá 110111, Colombia
| | - Jorge Alí-Torres
- Departamento de Química, Universidad Nacional de Colombia - Sede Bogotá, Bogotá 110111, Colombia
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4
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Sen S, Ali R, Onkar A, Verma S, Ahmad QT, Bhadauriya P, Sinha P, Nair NN, Ganesh S, Verma S. Synthesis of a highly thermostable insulin by phenylalanine conjugation at B29 Lysine. Commun Chem 2024; 7:161. [PMID: 39043846 PMCID: PMC11266353 DOI: 10.1038/s42004-024-01241-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
Globally, millions of diabetic patients require daily life-saving insulin injections. Insulin heat-lability and fibrillation pose significant challenges, especially in parts of the world without ready access to uninterrupted refrigeration. Here, we have synthesized four human insulin analogs by conjugating ε-amine of B29 lysine of insulin with acetic acid, phenylacetic acid, alanine, and phenylalanine residues. Of these, phenylalanine-conjugated insulin, termed FHI, was the most stable under high temperature (65 °C), elevated salt stress (25 mM NaCl), and varying pH levels (ranging from highly acidic pH 1.6 to physiological pH 7.4). It resists fibrillation for a significantly longer duration with sustained biological activity in in vitro, ex vivo, and in vivo and displays prolonged stability over its native counterpart. We further unravel the critical interactions, such as additional aromatic π-π interactions and hydrogen bonding in FHI, that are notably absent in native insulin. These interactions confer enhanced structural stability of FHI and offer a promising solution to the challenges associated with insulin heat sensitivity.
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Affiliation(s)
- Shantanu Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Rafat Ali
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Akanksha Onkar
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, 94143, CA, USA
| | - Shivani Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Quazi Taushif Ahmad
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Pratibha Bhadauriya
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Pradip Sinha
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
| | - Subramaniam Ganesh
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India
- Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology, Kanpur, 208016, UP, India
- Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, 208016, UP, India
| | - Sandeep Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, UP, India.
- Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology, Kanpur, 208016, UP, India.
- Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, 208016, UP, India.
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5
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Faran M, Ray D, Nag S, Raucci U, Parrinello M, Bisker G. A Stochastic Landscape Approach for Protein Folding State Classification. J Chem Theory Comput 2024; 20:5428-5438. [PMID: 38924770 PMCID: PMC11238538 DOI: 10.1021/acs.jctc.4c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Protein folding is a critical process that determines the functional state of proteins. Proper folding is essential for proteins to acquire their functional three-dimensional structures and execute their biological role, whereas misfolded proteins can lead to various diseases, including neurodegenerative disorders like Alzheimer's and Parkinson's. Therefore, a deeper understanding of protein folding is vital for understanding disease mechanisms and developing therapeutic strategies. This study introduces the Stochastic Landscape Classification (SLC), an innovative, automated, nonlearning algorithm that quantitatively analyzes protein folding dynamics. Focusing on collective variables (CVs) - low-dimensional representations of complex dynamical systems like molecular dynamics (MD) of macromolecules - the SLC approach segments the CVs into distinct macrostates, revealing the protein folding pathway explored by MD simulations. The segmentation is achieved by analyzing changes in CV trends and clustering these segments using a standard density-based spatial clustering of applications with noise (DBSCAN) scheme. Applied to the MD-based CV trajectories of Chignolin and Trp-Cage proteins, the SLC demonstrates apposite accuracy, validated by comparing standard classification metrics against ground-truth data. These metrics affirm the efficacy of the SLC in capturing intricate protein dynamics and offer a method to evaluate and select the most informative CVs. The practical application of this technique lies in its ability to provide a detailed, quantitative description of protein folding processes, with significant implications for understanding and manipulating protein behavior in industrial and pharmaceutical contexts.
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Affiliation(s)
- Michael Faran
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dhiman Ray
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen 83, 16152 Genova, Italy
| | - Shubhadeep Nag
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Umberto Raucci
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen 83, 16152 Genova, Italy
| | - Michele Parrinello
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen 83, 16152 Genova, Italy
| | - Gili Bisker
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- The
Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The
Center for Light-Matter Interaction, Tel
Aviv University, Tel Aviv 6997801, Israel
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6
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Tiroli-Cepeda AO, Linhares LA, Aragão AZB, de Jesus JR, Wasilewska-Sampaio AP, De Felice FG, Ferreira ST, Borges JC, Cyr DM, Ramos CHI. Type I Hsp40s/DnaJs aggregates exhibit features reminiscent of amyloidogenic structures. FEBS J 2024; 291:3904-3923. [PMID: 38975859 DOI: 10.1111/febs.17215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/14/2024] [Accepted: 06/20/2024] [Indexed: 07/09/2024]
Abstract
A rise in temperature triggers a structural change in the human Type I 40 kDa heat shock protein (Hsp40/DnaJ), known as DNAJA1. This change leads to a less compact structure, characterized by an increased presence of solvent-exposed hydrophobic patches and β-sheet-rich regions. This transformation is validated by circular dichroism, thioflavin T binding, and Bis-ANS assays. The formation of this β-sheet-rich conformation, which is amplified in the absence of zinc, leads to protein aggregation. This aggregation is induced not only by high temperatures but also by low ionic strength and high protein concentration. The aggregated conformation exhibits characteristics of an amyloidogenic structure, including a distinctive X-ray diffraction pattern, seeding competence (which stimulates the formation of amyloid-like aggregates), cytotoxicity, resistance to SDS, and fibril formation. Interestingly, the yeast Type I Ydj1 also tends to adopt a similar β-sheet-rich structure under comparable conditions, whereas Type II Hsp40s, whether human or from yeast, do not. Moreover, Ydj1 aggregates were found to be cytotoxic. Studies using DNAJA1- and Ydj1-deleted mutants suggest that the zinc-finger region plays a crucial role in amyloid formation. Our discovery of amyloid aggregation in a C-terminal deletion mutant of DNAJA1, which resembles a spliced homolog expressed in the testis, implies that Type I Hsp40 co-chaperones may generate amyloidogenic species in vivo.
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Affiliation(s)
- Ana O Tiroli-Cepeda
- Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Campinas, Brazil
| | - Leonardo A Linhares
- Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Campinas, Brazil
| | - Annelize Z B Aragão
- Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Campinas, Brazil
| | - Jemmyson R de Jesus
- Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Campinas, Brazil
| | | | - Fernanda G De Felice
- Institute of Medical Biochemistry Leopoldo de Meis, Rio de Janeiro, Brazil
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sérgio T Ferreira
- Institute of Medical Biochemistry Leopoldo de Meis, Rio de Janeiro, Brazil
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Júlio C Borges
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, Brazil
| | | | - Carlos H I Ramos
- Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Campinas, Brazil
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7
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Manav N, Jit BP, Kataria B, Sharma A. Cellular and epigenetic perspective of protein stability and its implications in the biological system. Epigenomics 2024; 16:879-900. [PMID: 38884355 PMCID: PMC11370918 DOI: 10.1080/17501911.2024.2351788] [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: 11/29/2023] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Protein stability is a fundamental prerequisite in both experimental and therapeutic applications. Current advancements in high throughput experimental techniques and functional ontology approaches have elucidated that impairment in the structure and stability of proteins is intricately associated with the cause and cure of several diseases. Therefore, it is paramount to deeply understand the physical and molecular confounding factors governing the stability of proteins. In this review article, we comprehensively investigated the evolution of protein stability, examining its emergence over time, its relationship with organizational aspects and the experimental methods used to understand it. Furthermore, we have also emphasized the role of Epigenetics and its interplay with post-translational modifications (PTMs) in regulating the stability of proteins.
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Affiliation(s)
- Nisha Manav
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Bimal Prasad Jit
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Babita Kataria
- Department of Medical Oncology, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
- Department of Biochemistry, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
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8
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Wei J, Meisl G, Dear A, Oosterhuis M, Melki R, Emanuelsson C, Linse S, Knowles TPJ. Kinetic models reveal the interplay of protein production and aggregation. Chem Sci 2024; 15:8430-8442. [PMID: 38846392 PMCID: PMC11151821 DOI: 10.1039/d4sc00088a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Protein aggregation is a key process in the development of many neurodegenerative disorders, including dementias such as Alzheimer's disease. Significant progress has been made in understanding the molecular mechanisms of aggregate formation in pure buffer systems, much of which was enabled by the development of integrated rate laws that allowed for mechanistic analysis of aggregation kinetics. However, in order to translate these findings into disease-relevant conclusions and to make predictions about the effect of potential alterations to the aggregation reactions by the addition of putative inhibitors, the current models need to be extended to account for the altered situation encountered in living systems. In particular, in vivo, the total protein concentrations typically do not remain constant and aggregation-prone monomers are constantly being produced but also degraded by cells. Here, we build a theoretical model that explicitly takes into account monomer production, derive integrated rate laws and discuss the resulting scaling laws and limiting behaviours. We demonstrate that our models are suited for the aggregation-prone Huntington's disease-associated peptide HttQ45 utilizing a system for continuous in situ monomer production and the aggregation of the tumour suppressor protein P53. The aggregation-prone HttQ45 monomer was produced through enzymatic cleavage of a larger construct in which a fused protein domain served as an internal inhibitor. For P53, only the unfolded monomers form aggregates, making the unfolding a rate-limiting step which constitutes a source of aggregation-prone monomers. The new model opens up possibilities for a quantitative description of aggregation in living systems, allowing for example the modelling of inhibitors of aggregation in a dynamic environment of continuous protein synthesis.
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Affiliation(s)
- Jiapeng Wei
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Alexander Dear
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Biochemistry and Structural Biology, Lund University SE22100 Lund Sweden
| | - Matthijs Oosterhuis
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS 18 Route du Panorama, Fontenay-Aux-Roses cedex 92265 France
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University Lund Sweden
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cavendish Laboratory, University of Cambridge J J Thomson Avenue CB3 0HE UK
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9
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Miller EM, Chan TCD, Montes-Matamoros C, Sharif O, Pujo-Menjouet L, Lindstrom MR. Oscillations in Neuronal Activity: A Neuron-Centered Spatiotemporal Model of the Unfolded Protein Response in Prion Diseases. Bull Math Biol 2024; 86:82. [PMID: 38837083 DOI: 10.1007/s11538-024-01307-y] [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: 12/30/2023] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Abstract
Many neurodegenerative diseases (NDs) are characterized by the slow spatial spread of toxic protein species in the brain. The toxic proteins can induce neuronal stress, triggering the Unfolded Protein Response (UPR), which slows or stops protein translation and can indirectly reduce the toxic load. However, the UPR may also trigger processes leading to apoptotic cell death and the UPR is implicated in the progression of several NDs. In this paper, we develop a novel mathematical model to describe the spatiotemporal dynamics of the UPR mechanism for prion diseases. Our model is centered around a single neuron, with representative proteins P (healthy) and S (toxic) interacting with heterodimer dynamics (S interacts with P to form two S's). The model takes the form of a coupled system of nonlinear reaction-diffusion equations with a delayed, nonlinear flux for P (delay from the UPR). Through the delay, we find parameter regimes that exhibit oscillations in the P- and S-protein levels. We find that oscillations are more pronounced when the S-clearance rate and S-diffusivity are small in comparison to the P-clearance rate and P-diffusivity, respectively. The oscillations become more pronounced as delays in initiating the UPR increase. We also consider quasi-realistic clinical parameters to understand how possible drug therapies can alter the course of a prion disease. We find that decreasing the production of P, decreasing the recruitment rate, increasing the diffusivity of S, increasing the UPR S-threshold, and increasing the S clearance rate appear to be the most powerful modifications to reduce the mean UPR intensity and potentially moderate the disease progression.
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Affiliation(s)
- Elliot M Miller
- College of Arts and Sciences, Culverhouse College of Business, The University of Alabama, Tuscaloosa, AL, USA
| | - Tat Chung D Chan
- Department of Mathematics, University of California Berkeley, Berkeley, CA, USA
| | - Carlos Montes-Matamoros
- School of Mathematical and Statistical Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Omar Sharif
- School of Mathematical and Statistical Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Laurent Pujo-Menjouet
- Universite Claude Bernard Lyon 1, CNRS, Ecole Centrale de Lyon, INSA Lyon, Université Jean Monnet, ICJ UMR5208, Inria, 69622, Villeurbanne, France
| | - Michael R Lindstrom
- School of Mathematical and Statistical Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, USA.
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10
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Hemagirri M, Chen Y, Gopinath SCB, Sahreen S, Adnan M, Sasidharan S. Crosstalk between protein misfolding and endoplasmic reticulum stress during ageing and their role in age-related disorders. Biochimie 2024; 221:159-181. [PMID: 37918463 DOI: 10.1016/j.biochi.2023.10.019] [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: 07/31/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Maintaining the proteome is crucial to retaining cell functionality and response to multiple intrinsic and extrinsic stressors. Protein misfolding increased the endoplasmic reticulum (ER) stress and activated the adaptive unfolded protein response (UPR) to restore cell homeostasis. Apoptosis occurs when ER stress is prolonged or the adaptive response fails. In healthy young cells, the ratio of protein folding machinery to quantities of misfolded proteins is balanced under normal circumstances. However, the age-related deterioration of the complex systems for handling protein misfolding is accompanied by ageing-related disruption of protein homeostasis, which results in the build-up of misfolded and aggregated proteins. This ultimately results in decreased cell viability and forms the basis of common age-related diseases called protein misfolding diseases. Proteins or protein fragments convert from their ordinarily soluble forms to insoluble fibrils or plaques in many of these disorders, which build up in various organs such as the liver, brain, or spleen. Alzheimer's, Parkinson's, type II diabetes, and cancer are diseases in this group commonly manifest in later life. Thus, protein misfolding and its prevention by chaperones and different degradation paths are becoming understood from molecular perspectives. Proteodynamics information will likely affect future interventional techniques to combat cellular stress and support healthy ageing by avoiding and treating protein conformational disorders. This review provides an overview of the diverse proteostasis machinery, protein misfolding, and ER stress involvement, which activates the UPR sensors. Here, we will discuss the crosstalk between protein misfolding and ER stress and their role in developing age-related diseases.
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Affiliation(s)
- Manisekaran Hemagirri
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Yeng Chen
- Department of Oral & Craniofacial Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Subash C B Gopinath
- Faculty of Chemical Engineering and Technology, Universiti Malaysia Perlis, Arau, 02600, Malaysia
| | - Sumaira Sahreen
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, P. O. Box 2440, Saudi Arabia.
| | - Sreenivasan Sasidharan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, USM, 11800, Pulau Pinang, Malaysia.
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11
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Dolui S, Roy A, Pal U, Kundu S, Pandit E, N Ratha B, Pariary R, Saha A, Bhunia A, Maiti NC. Raman Spectroscopic Insights of Phase-Separated Insulin Aggregates. ACS PHYSICAL CHEMISTRY AU 2024; 4:268-280. [PMID: 38800728 PMCID: PMC11117687 DOI: 10.1021/acsphyschemau.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/29/2024]
Abstract
Phase-separated protein accumulation through the formation of several aggregate species is linked to the pathology of several human disorders and diseases. Our current investigation envisaged detailed Raman signature and structural intricacy of bovine insulin in its various forms of aggregates produced in situ at an elevated temperature (60 °C). The amide I band in the Raman spectrum of the protein in its native-like conformation appeared at 1655 cm-1 and indicated the presence of a high content of α-helical structure as prepared freshly in acidic pH. The disorder content (turn and coils) also was predominately present in both the monomeric and oligomeric states and was confirmed by the presence shoulder amide I maker band at ∼1680 cm-1. However, the band shifted to ∼1671 cm-1 upon the transformation of the protein solution into fibrillar aggregates as produced for a longer time of incubation. The protein, however, maintained most of its helical conformation in the oligomeric phase; the low-frequency backbone α-helical conformation signal at ∼935 cm-1 was similar to that of freshly prepared aqueous protein solution enriched in helical conformation. The peak intensity was significantly weak in the fibrillar aggregates, and it appeared as a good Raman signature to follow the phase separation and the aggregation behavior of insulin and similar other proteins. Tyrosine phenoxy moieties in the protein may maintained its H-bond donor-acceptor integrity throughout the course of fibril formation; however, it entered in more hydrophobic environment in its journey of fibril formation. In addition, it was noticed that oligomeric bovine insulin maintained the orientation/conformation of the disulfide bonds. However, in the fibrillar state, the disulfide linkages became more strained and preferred to maintain a single conformation state.
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Affiliation(s)
- Sandip Dolui
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anupam Roy
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Uttam Pal
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Shubham Kundu
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Esha Pandit
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Bhisma N Ratha
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Ranit Pariary
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Achintya Saha
- Department
of Chemical Technology, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009, India
| | - Anirban Bhunia
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Nakul C. Maiti
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
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12
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Zaidi N, Ahmad O, Khursheed M, Nabi F, Uversky VN, Khan RH. Furosemide Derails Human Lysozyme Fibrillation by Interacting with Aggregation Hot Spots: A Biophysical Comprehension. J Phys Chem B 2024; 128:4283-4300. [PMID: 38683125 DOI: 10.1021/acs.jpcb.3c02613] [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: 05/01/2024]
Abstract
Kidney-associated human lysozyme amyloidosis leads to renal impairments;thus, patients are often prescribed furosemide. Based on this fact, the effect of furosemide on induced human lysozyme fibrillation, in vitro, is evaluated by spectroscopic, calorimetric, computational, and cellular-based assays/methods. Results show that furosemide increases the lag phase and decreases the apparent rate of aggregation of human lysozyme, thereby decelerating the nucleation phase and amyloid fibril formation, as confirmed by the decrease in the level of Thioflavin-T fluorescence. Fewer entities of hydrodynamic radii of ∼171 nm instead of amyloid fibrils (∼412 nm) are detected in human lysozyme in the presence of furosemide by dynamic light scattering. Moreover, furosemide decreases the extent of conversion of the α/β structure of human lysozyme into a predominant β-sheet. The isothermal titration calorimetry established that furosemide forms a complex with human lysozyme, which was also confirmed through fluorescence quenching and computational studies. Also, human lysozyme lytic activity is inhibited competitively by furosemide due to the involvement of amino acid residues of the active site in catalysis, as well as complex formation. Conclusively, furosemide interacts with Gln58, Ile59, Asn60, Ala108, and Trp109 of aggregation-prone regions 2 and 4 of human lysozyme, thereby masking its sites of aggregation and generating only lower-order entities that are less toxic to red blood cells than the fibrils. Thus, furosemide slows the progression of amyloid fibrillation in human lysozyme.
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Affiliation(s)
- Nida Zaidi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Owais Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Maryam Khursheed
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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13
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Fan J, Liang L, Zhou X, Ouyang Z. Accelerating protein aggregation and amyloid fibrillation for rapid inhibitor screening. Chem Sci 2024; 15:6853-6859. [PMID: 38725489 PMCID: PMC11077537 DOI: 10.1039/d4sc00437j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/04/2024] [Indexed: 05/12/2024] Open
Abstract
The accumulation and deposition of amyloid fibrils, also known as amyloidosis, in tissues and organs of patients has been found to be linked to numerous devastating neurodegenerative diseases. The aggregation of proteins to form amyloid fibrils, however, is a slow pathogenic process, and is a major issue for the evaluation of the effectiveness of inhibitors in new drug discovery and screening. Here, we used microdroplet reaction technology to accelerate the amyloid fibrillation process, monitored the process to shed light on the fundamental mechanism of amyloid self-assembly, and demonstrated the value of the technology in the rapid screening of potential inhibitor drugs. Proteins in microdroplets accelerated to form fibrils in milliseconds, enabling an entire cycle of inhibitor screening for Aβ40 within 3 minutes. The technology would be of broad interest to drug discovery and therapeutic design to develop treatments for diseases associated with protein aggregation and fibrillation.
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Affiliation(s)
- Jingjin Fan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Liwen Liang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
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14
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Ding F, Sun Q, Long C, Rasmussen RN, Peng S, Xu Q, Kang N, Song W, Weikop P, Goldman SA, Nedergaard M. Dysregulation of extracellular potassium distinguishes healthy ageing from neurodegeneration. Brain 2024; 147:1726-1739. [PMID: 38462589 PMCID: PMC11068329 DOI: 10.1093/brain/awae075] [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: 11/01/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 03/12/2024] Open
Abstract
Progressive neuronal loss is a hallmark feature distinguishing neurodegenerative diseases from normal ageing. However, the underlying mechanisms remain unknown. Extracellular K+ homeostasis is a potential mediator of neuronal injury as K+ elevations increase excitatory activity. The dysregulation of extracellular K+ and potassium channel expressions during neurodegeneration could contribute to this distinction. Here we measured the cortical extracellular K+ concentration ([K+]e) in awake wild-type mice as well as murine models of neurodegeneration using K+-sensitive microelectrodes. Unexpectedly, aged wild-type mice exhibited significantly lower cortical [K+]e than young mice. In contrast, cortical [K+]e was consistently elevated in Alzheimer's disease (APP/PS1), amyotrophic lateral sclerosis (ALS) (SOD1G93A) and Huntington's disease (R6/2) models. Cortical resting [K+]e correlated inversely with neuronal density and the [K+]e buffering rate but correlated positively with the predicted neuronal firing rate. Screening of astrocyte-selective genomic datasets revealed a number of potassium channel genes that were downregulated in these disease models but not in normal ageing. In particular, the inwardly rectifying potassium channel Kcnj10 was downregulated in ALS and Huntington's disease models but not in normal ageing, while Fxyd1 and Slc1a3, each of which acts as a negative regulator of potassium uptake, were each upregulated by astrocytes in both Alzheimer's disease and ALS models. Chronic elevation of [K+]e in response to changes in gene expression and the attendant neuronal hyperexcitability may drive the neuronal loss characteristic of these neurodegenerative diseases. These observations suggest that the dysregulation of extracellular K+ homeostasis in a number of neurodegenerative diseases could be due to aberrant astrocytic K+ buffering and as such, highlight a fundamental role for glial dysfunction in neurodegeneration.
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Affiliation(s)
- Fengfei Ding
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Pharmacology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qian Sun
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Pharmacology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Carter Long
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Rune Nguyen Rasmussen
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sisi Peng
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Qiwu Xu
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ning Kang
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Wei Song
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Pia Weikop
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for Basic and Translational Neuroscience, Faculty of Health and Medical Sciences, Neurology Department, University of Copenhagen, 2200 Copenhagen, Denmark
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15
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Takamuku T, Haraguchi T, Sasaki R, Hozoji Y, Sadakane K, Iwase H. Alcohol-Induced Denaturation of Hen Egg White Lysozyme Studied by Infrared, Circular Dichroism, and Small-Angle Neutron Scattering. J Phys Chem B 2024; 128:4076-4086. [PMID: 38642057 DOI: 10.1021/acs.jpcb.4c00209] [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: 04/22/2024]
Abstract
In aqueous binary solvents with fluorinated alcohols, 2,2,2-trifluoroethanol (TFE) and 1,1,1,3,3,3-hexafluoroisopropanol (HFIP), and aliphatic alcohols, ethanol (EtOH) and 2-propanol (2-PrOH), the denaturation of hen egg white lysozyme (HEWL) with increasing alcohol mole fraction xA has been investigated in a wide view from the molecular vibration to the secondary and ternary structures. Circular dichroism (CD) measurement showed that the secondary structure of α-helix content of HEWL increases on adding a small amount of the fluorinated alcohol to the aqueous solution, while the β-sheet content decreases. On the contrary, the secondary structure does not significantly change by the addition of the aliphatic alcohols. Correspondingly, the infrared (IR) spectroscopic measurements revealed that the amide I band red-shifts on the addition of the fluorinated alcohol. However, the band remains unchanged in the aliphatic alcohol systems with increasing alcohol content. To observe the ternary structure of HEWL, small-angle neutron scattering (SANS) experiments with H/D substitution technique have been applied to the HEWL solutions. The SANS experiments were successful in revealing the details of how the geometry of the HEWL changes as a function of xA. The SANS profiles indicated the spherical structure of HEWL in all of the alcohol systems in the xA range examined. The mean radius of HEWL in the two fluorinated alcohol systems increases from ∼16 to ∼18 Å during the change in the secondary structure against the increase in the fluorinated alcohol content. On contrast, the radius does not significantly change in both aliphatic alcohol systems below xA = 0.3 but expands to ∼19 Å as the alcohol content is close to the limitation of the HEWL solubility. According to the present results, together with our knowledge of the alcohol cluster formation and the interaction of the trifluoromethyl (CF3) groups with the hydrophobic moieties of biomolecules, the effects of alcohols on the denaturation of the protein have been discussed on a molecular scale.
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Affiliation(s)
- Toshiyuki Takamuku
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Tomoya Haraguchi
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Ryu Sasaki
- Functional Biomolecular Science, Graduate School of Advanced Health Sciences, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Yusuke Hozoji
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe, Kyoto 610-0394, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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16
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Das A, Jana G, Sing S, Basu A. Insights into the interaction and inhibitory action of palmatine on lysozyme fibrillogenesis: Spectroscopic and computational studies. Int J Biol Macromol 2024; 268:131703. [PMID: 38643915 DOI: 10.1016/j.ijbiomac.2024.131703] [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: 01/29/2024] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
Interaction under amyloidogenic condition between naturally occurring protoberberine alkaloid palmatine and hen egg white lysozyme was executed by adopting spectrofluorometric and theoretical molecular docking and dynamic simulation analysis. In spetrofluorometric method, different types of experiments were performed to explore the overall mode and mechanism of interaction. Intrinsic fluorescence quenching of lysozyme (Trp residues) by palmatine showed effective binding interaction and also yielded different binding parameters like binding constant, quenching constant and number of binding sites. Synchronous fluorescence quenching and 3D fluorescence map revealed that palmatine was able to change the microenvironment of the interacting site. Fluorescence life time measurements strongly suggested that this interaction was basically static in nature. Molecular docking result matched with fluorimetric experimental data. Efficient drug like interaction of palmatine with lysozyme at low pH and high salt concentration prompted us to analyze its antifibrillation potential. Different assays and microscopic techniques were employed for detailed analysis of lysozyme amyloidosis.Thioflavin T(ThT) assay, Congo Red (CR) assay, 8-anilino-1-naphthalenesulfonic acid (ANS) assay, Nile Red (NR) assay, anisotropy and intrinsic fluorescence measurements confirmed that palmatine successfully retarded and reduced lysozyme fibrillation. Dynamic light scattering (DLS) and atomic force microscopy (AFM) further reiterated the excellent antiamyloidogenic potency of palmatine.
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Affiliation(s)
- Arindam Das
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore 721 102, India
| | - Gouranga Jana
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore 721 102, India
| | - Shukdeb Sing
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore 721 102, India
| | - Anirban Basu
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore 721 102, India.
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17
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López-Bascón MA, Moscoso-Ruiz I, Quirantes-Piné R, del Pino-García R, López-Gámez G, Justicia-Rueda A, Verardo V, Quiles JL. Characterization of Phenolic Compounds in Extra Virgin Olive Oil from Granada (Spain) and Evaluation of Its Neuroprotective Action. Int J Mol Sci 2024; 25:4878. [PMID: 38732097 PMCID: PMC11084348 DOI: 10.3390/ijms25094878] [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: 03/22/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
The olive oil sector is a fundamental food in the Mediterranean diet. It has been demonstrated that the consumption of extra virgin olive oil (EVOO) with a high content of phenolic compounds is beneficial in the prevention and/or treatment of many diseases. The main objective of this work was to study the relationship between the content of phenolic compounds and the in vitro neuroprotective and anti-inflammatory activity of EVOOs from two PDOs in the province of Granada. To this purpose, the amounts of phenolic compounds were determined by liquid chromatography coupled to mass spectrometry (HPLC-MS) and the inhibitory activity of acetylcholinesterase (AChE) and cyclooxygenase-2 (COX-2) enzymes by spectrophotometric and fluorimetric assays. The main families identified were phenolic alcohols, secoiridoids, lignans, flavonoids, and phenolic acids. The EVOO samples with the highest total concentration of compounds and the highest inhibitory activity belonged to the Picual and Manzanillo varieties. Statistical analysis showed a positive correlation between identified compounds and AChE and COX-2 inhibitory activity, except for lignans. These results confirm EVOO's compounds possess neuroprotective potential.
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Affiliation(s)
- María Asunción López-Bascón
- Centro de Investigación y Desarrollo del Alimento Funcional (CIDAF), Avda. Del Conocimiento, 37, 18016 Granada, Spain; (M.A.L.-B.)
| | - Inmaculada Moscoso-Ruiz
- Centro de Investigación y Desarrollo del Alimento Funcional (CIDAF), Avda. Del Conocimiento, 37, 18016 Granada, Spain; (M.A.L.-B.)
| | - Rosa Quirantes-Piné
- Department of Analytical Chemistry, University of Granada, Avda. Fuentenueva S/N, 18071 Granada, Spain;
| | - Raquel del Pino-García
- Centro de Investigación y Desarrollo del Alimento Funcional (CIDAF), Avda. Del Conocimiento, 37, 18016 Granada, Spain; (M.A.L.-B.)
| | - Gloria López-Gámez
- Centro de Investigación y Desarrollo del Alimento Funcional (CIDAF), Avda. Del Conocimiento, 37, 18016 Granada, Spain; (M.A.L.-B.)
| | - Andrea Justicia-Rueda
- Centro de Investigación y Desarrollo del Alimento Funcional (CIDAF), Avda. Del Conocimiento, 37, 18016 Granada, Spain; (M.A.L.-B.)
| | - Vito Verardo
- Centro de Investigación y Desarrollo del Alimento Funcional (CIDAF), Avda. Del Conocimiento, 37, 18016 Granada, Spain; (M.A.L.-B.)
- Department of Nutrition and Food Science, Institute of Nutrition and Food Technology “José Mataix Verdú”, Biomedical Research Centre, University of Granada, 18071 Granada, Spain
| | - José L. Quiles
- Department of Physiology, Institute of Nutrition and Food Technology “José Mataix Verdú”, Biomedical Research Centre, University of Granada, 18016 Armilla, Spain
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, Isabel Torres, 21, 39011 Santander, Spain
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18
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Leventhal MJ, Zanella CA, Kang B, Peng J, Gritsch D, Liao Z, Bukhari H, Wang T, Pao PC, Danquah S, Benetatos J, Nehme R, Farhi S, Tsai LH, Dong X, Scherzer CR, Feany MB, Fraenkel E. A systems-biology approach connects aging mechanisms with Alzheimer's disease pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585262. [PMID: 38559190 PMCID: PMC10980014 DOI: 10.1101/2024.03.17.585262] [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: 04/04/2024]
Abstract
Age is the strongest risk factor for developing Alzheimer's disease, the most common neurodegenerative disorder. However, the mechanisms connecting advancing age to neurodegeneration in Alzheimer's disease are incompletely understood. We conducted an unbiased, genome-scale, forward genetic screen for age-associated neurodegeneration in Drosophila to identify the underlying biological processes required for maintenance of aging neurons. To connect genetic screen hits to Alzheimer's disease pathways, we measured proteomics, phosphoproteomics, and metabolomics in Drosophila models of Alzheimer's disease. We further identified Alzheimer's disease human genetic variants that modify expression in disease-vulnerable neurons. Through multi-omic, multi-species network integration of these data, we identified relationships between screen hits and tau-mediated neurotoxicity. Furthermore, we computationally and experimentally identified relationships between screen hits and DNA damage in Drosophila and human iPSC-derived neural progenitor cells. Our work identifies candidate pathways that could be targeted to attenuate the effects of age on neurodegeneration and Alzheimer's disease.
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Affiliation(s)
- Matthew J Leventhal
- MIT Ph.D. Program in Computational and Systems Biology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Camila A Zanella
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Byunguk Kang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Jiajie Peng
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - David Gritsch
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhixiang Liao
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Hassan Bukhari
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tao Wang
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Present address: School of Computer Science, Northwestern Polytechnical University, Xi’an, China
| | - Ping-Chieh Pao
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Joseph Benetatos
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Samouil Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Li-Huei Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xianjun Dong
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Clemens R Scherzer
- Precision Neurology Program, Brigham and Women’s Hospital and Harvard Medical school, Boston, MA, USA
- APDA Center for Advanced Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Present address: Stephen and Denise Adams Center of Yale School of Medicine, CT, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Ernest Fraenkel
- MIT Ph.D. Program in Computational and Systems Biology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Lead contact
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19
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Anselmo S, Sancataldo G, Vetri V. Deciphering amyloid fibril molecular maturation through FLIM-phasor analysis of thioflavin T. BIOPHYSICAL REPORTS 2024; 4:100145. [PMID: 38404533 PMCID: PMC10884809 DOI: 10.1016/j.bpr.2024.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024]
Abstract
The investigation of amyloid fibril formation is paramount for advancing our understanding of neurodegenerative diseases and for exploring potential correlated therapeutic strategies. Moreover, the self-assembling properties of amyloid fibrils show promise for the development of advanced protein-based biomaterials. Among the methods employed to monitor protein aggregation processes, fluorescence has emerged as a powerful tool. Its exceptional sensitivity enables the detection of early-stage aggregation events that are otherwise challenging to observe. This research underscores the pivotal role of fluorescence analysis, particularly in investigating the aggregation processes of hen egg white lysozyme, a model protein extensively studied for insights into amyloid fibril formation. By combining classical spectroscopies with fluorescence microscopy and by exploiting the fluorescence properties (intensity and lifetime) of the thioflavin T, we were able to noninvasively monitor key and complex molecular aspects of the process. Intriguingly, the fluorescence lifetime imaging-phasor analysis of thioflavin T fluorescence lifetime on structures at different stages of aggregation allowed to decipher the complex fluorescence decay behavior, highlighting that their changes rise from the combination of specific binding to amyloid typical cross-β structures and of the rigidity of the molecular environment.
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Affiliation(s)
- Sara Anselmo
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
| | - Giuseppe Sancataldo
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
| | - Valeria Vetri
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
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20
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Adasme-Carreño F, Ochoa-Calle A, Galván M, Ireta J. Conformational preference of dipeptide zwitterions in aqueous solvents. Phys Chem Chem Phys 2024; 26:8210-8218. [PMID: 38384231 DOI: 10.1039/d3cp05742a] [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: 02/23/2024]
Abstract
Proper description of solvent effects is challenging for theoretical methods, particularly if the solute is a zwitterion. Here, a series of theoretical procedures are used to determine the preferred solvated conformations of twelve hydrophobic dipeptides (Leu-Leu, Leu-Phe, Phe-Leu, Ile-Leu, Phe-Phe, Ala-Val, Val-Ala, Ala-Ile, Ile-Ala, Ile-Val, Val-Ile and Val-Val) in the zwitterionic state. First, the accuracy of density functional theory (DFT), combined with different implicit solvent models, for describing zwitterions in aqueous solvent is assessed by comparing the predicted against the experimental glycine tautomerization energy, i.e., the energetic difference between canonical and zwitterionic glycine in aqueous solvents. It is found that among the tested solvation schemes, the charge-asymmetric nonlocally determined local-electric solvation model (CANDLE) predicts an energetic difference in excellent agreement with the experimental value. Next, DFT-CANDLE is used to determine the most favorable solvated conformation for each of the investigated dipeptide zwitterions. The CANDLE-solvated structures are obtained by exploring the conformational space of each dipeptide zwitterion concatenating DFT calculations, in vacuum, with classical molecular dynamics simulations, in explicit solvents, and DFT calculations including explicit water molecules. It is found that the energetically most favorable conformations are similar to those of the dipeptide zwitterions in their respective crystal structures. Such structural agreement is indicative of the DFT-CANDLE accomplishment of the description of solvated zwitterions, and suggests that these biomolecules self-assemble as quasi-rigid objects.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectorá de Investigación y Postgrado Universidad Católica del Maule, Talca 3480112, Chile.
- Laboratorio de Bioinformática y Química Computacional (LBQC), Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480112, Chile
| | - Alvaro Ochoa-Calle
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Marcelo Galván
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
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21
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Chang YJ, Chien YH, Chang CC, Wang PN, Chen YR, Chang YC. Detection of Femtomolar Amyloid-β Peptides for Early-Stage Identification of Alzheimer's Amyloid-β Aggregation with Functionalized Gold Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2024; 16:3819-3828. [PMID: 38214471 DOI: 10.1021/acsami.3c12750] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Progressive amyloid-β (Aβ) fibrillar aggregates have long been considered as the pathogenesis of Alzheimer's disease (AD). Biocompatible and stable cysteine-Aβ peptide-conjugated gold nanoparticles (Cys-Aβ@AuNP) are demonstrated as suitable materials for detecting subfemtomolar Aβ peptides in human plasma. Incubation with Aβ peptides causes the Cys-Aβ@AuNP to aggregate and changes its absorption spectra. The spectral change is especially apparent and noticeable when detecting subfemtomolar Aβ peptides, and the aggregates contain only two or three AuNPs. Cys-Aβ@AuNP can also be used to identify early-stage Aβ oligomerization, which is not possible using the conventional method, in which the fluorescence of thioflavin-T is measured. The ability to detect Aβ oligomerization can facilitate therapeutics for AD. In addition, the binding of Aβ peptides by Cys-Aβ@AuNP in combination with centrifugation redirects the conventional Aβ aggregation pathway and can effectively inhibit the formation of toxic Aβ oligomers or fibrils. Therefore, the proposed Cys-Aβ@AuNP can also be used to develop effective therapeutic agents to inhibit Aβ aggregation. The results obtained in this study are expected to open revolutionary ways to both detect and inhibit Aβ aggregation at an early stage.
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Affiliation(s)
- Yu-Jen Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
| | - Yi-Hsin Chien
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Chieh-Chun Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Physics, National Taiwan University, Taipei 106, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, and National Taiwan University, Taipei 115, Taiwan
| | - Pei-Ning Wang
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Division of General Neurology, Department of Neurological Institute, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
| | - Yun-Chorng Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei 115, Taiwan
- Department of Physics, National Taiwan University, Taipei 106, Taiwan
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, and National Taiwan University, Taipei 115, Taiwan
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22
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Serravalle S, Pisano M, Sciacca MFM, Salamone N, Sicali L, Mazzara G, Costa L, La Rosa C. Critical micellar concentration determination of pure phospholipids and lipid-raft and their mixtures with cholesterol. Proteins 2024. [PMID: 38234101 DOI: 10.1002/prot.26669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/01/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Phospholipids in biological membranes establish a chemical equilibrium between free phospholipids in the aqueous phase (CMC) and self-assembled phospholipids in vesicles, keeping the CMC constant. The CMC is different for each phospholipid, depends on the amount of cholesterol, and, according to the lipid-chaperone hypothesis, controls the interaction between free phospholipids and amyloidogenic proteins (such as amylin, amyloid-β, and α-synuclein, all of which are, respectively, associated with a different proteinopathy), which governs the formation of a toxic complex between free lipids and proteins that leads to membrane destruction. Here, we provide quantitative measurements of CMCs and bilayer stability of pure phospholipids, lipid rafts, and their mixture with cholesterol by fluorescence methods (using pyrene as a probe) and light scattering techniques (resonance Rayleigh scattering and fixed-angle light scattering) performed on LUVs, as well as AFM to measure LUV dimensions. Also, we test the lipid-chaperone hypothesis on human IAPP interacting with different mixture of POPC cholesterol. Stated the importance of CMC in membrane stability and protein aggregation processes, these results could be a starting point for the development of a quantitative kinetic model for the lipid chaperone hypothesis.
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Affiliation(s)
- Sofia Serravalle
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Martina Pisano
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Michele F M Sciacca
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Nancy Salamone
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Luciano Sicali
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Giuseppe Mazzara
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Luca Costa
- Centre de Biologie Structurale, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Carmelo La Rosa
- Department of Chemical Sciences, University of Catania, Catania, Italy
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23
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Guan Y, Li Y, Gao W, Mei J, Xu W, Wang C, Ai H. Aggregation Dynamics Characteristics of Seven Different Aβ Oligomeric Isoforms-Dependence on the Interfacial Interaction. ACS Chem Neurosci 2024; 15:155-168. [PMID: 38109178 DOI: 10.1021/acschemneuro.3c00585] [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: 12/19/2023] Open
Abstract
The aggregation of β-amyloid (Aβ) peptides has been confirmed to be associated with the onset of Alzheimer's disease (AD). Among the three phases of Aβ aggregation, the lag phase has been considered to be the best time for early Aβ pathological deposition clinical intervention and prevention for potential patients with normal cognition. Aβ peptide exists in various lengths in vivo, and Aβ oligomer in the early lag phase is neurotoxic but polymorphous and metastable, depending on Aβ length (isoform), molecular weight, and specific phase, and therefore hardly characterized experimentally. To cope with the problem, molecular dynamics simulation was used to investigate the aggregation process of five monomers for each of the seven common Aβ isoforms during the lag phase. Results showed that Aβ(1-40) and Aβ(1-38) monomers aggregated faster than their truncated analogues Aβ(4-40) and Aβ(4-38), respectively. However, the aggregation rate of Aβ(1-42) was slower than that of its truncated analogues Aβ(4-42) rather than that of Aβpe(3-42). More importantly, Aβ(1-38) is first predicted as more likely to form stable hexamer than the remaining five Aβ isoforms, as Aβ(1-42) does. It is hydrophobic interaction mainly (>50%) from the interfacial β1 and β2 regions of two reactants, pentamer and monomer, aggregated by Aβ(1-38)/Aβ(1-42) rather than by other Aβ isoforms, that drives the hexamer stably as a result of the formation of the effective hydrophobic collapse. This paper provides new insights into the aggregation characteristics of Aβ with different lengths and the conditions necessary for Aβ to form oligomers with a high molecular weight in the early lag phase, revealing the dependence of Aβ hexamer formation on the specific interfacial interaction.
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Affiliation(s)
- Yvning Guan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Ye Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Wenqi Gao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Jinfei Mei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Wen Xu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Chuanbo Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Hongqi Ai
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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24
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Warerkar OD, Mudliar NH, Momin MM, Singh PK. Targeting Amyloids with Coated Nanoparticles: A Review on Potential Combinations of Nanoparticles and Bio-Compatible Coatings. Crit Rev Ther Drug Carrier Syst 2024; 41:85-119. [PMID: 37938191 DOI: 10.1615/critrevtherdrugcarriersyst.2023046209] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Amyloidosis is the major cause of many neurodegenerative diseases, such as, Alzheimer's and Parkinson's where the misfolding and deposition of a previously functional protein make it inept for carrying out its function. The genesis of amyloid fibril formation and the strategies to inhibit it have been studied extensively, although some parts of this puzzle still remain unfathomable to date. Many classes of molecules have been explored as potential drugs in vitro, but their inability to work in vivo by crossing the blood-brain-barrier has made them an inadequate treatment option. In this regard, nanoparticles (NPs) have turned out to be an exciting alternative because they could overcome many drawbacks of previously studied molecules and provide advantages, such as, greater bioavailability of molecules and target-specific delivery of drugs. In this paper, we present an overview on several coated NPs which have shown promising efficiency in inhibiting fibril formation. A hundred and thirty papers published in the past two decades have been comprehensively reviewed, which majorly encompass NPs comprising different materials like gold, silver, iron-oxide, poly(lactic-co-glycolic acid), polymeric NP, etc., which are coated with various molecules of predominantly natural origin, such as different types of amino acids, peptides, curcumin, drugs, catechin, etc. We hope that this review will shed light on the advancement of symbiotic amalgamation of NPs with molecules from natural sources and will inspire further research on the tremendous therapeutic potential of these combinations for many amyloid-related diseases.
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Affiliation(s)
- Oshin D Warerkar
- SVKM's Shri C.B. Patel Research Centre, Vile Parle, Mumbai, Maharashtra 400056, India
| | - Niyati H Mudliar
- SVKM's Shri C.B. Patel Research Centre, Vile Parle, Mumbai, Maharashtra 400056, India
| | - Munira M Momin
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, Maharashtra, India; SVKM's Shri C.B. Patel Research Centre for Chemistry and Biological Sciences, Vile Parle (West), Mumbai, Maharashtra, 400056, India
| | - Prabhat K Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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25
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Kurniawan J, Ishida T. Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets. J Chem Inf Model 2023; 63:6778-6788. [PMID: 37897811 DOI: 10.1021/acs.jcim.3c00750] [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: 10/30/2023]
Abstract
Accurate prediction of protein stability upon a point mutation has important applications in drug discovery and personalized medicine. It remains a challenging issue in computational biology. Existing computational prediction methods, which range from mechanistic to supervised learning approaches, have experienced limited progress over the last few decades. This stagnation is largely due to their heavy reliance on both the quantity and quality of the training data. This is evident in recent state-of-the-art methods that continue to yield substantial errors on two challenging blind test sets: frataxin and p53, with average root-mean-square errors exceeding 3 and 1.5 kcal/mol, respectively, which is still above the theoretical 1 kcal/mol prediction barrier. Rigorous approaches, on the other hand, offer greater potential for accuracy without relying on training data but are computationally demanding and require both wild-type and mutant structure information. Although they showed high accuracy for conserving mutations, their performance is still limited for charge-changing mutation cases. This might be due to the lack of an available mutant structure, often represented by a simplified capped peptide. The recent advances in protein structure prediction methods now make it possible to obtain structures comparable to experimental ones, including complete mutant structure information. In this work, we compare the performance of supervised learning-based methods and rigorous approaches for predicting protein stability on point mutations in difficult targets: frataxin and p53. The rigorous alchemical method significantly surpasses state-of-the-art techniques in terms of both the root-mean-squared error and Pearson correlation coefficient in these two challenging blind test sets. Additionally, we propose an improved alchemical method that employs the pmx double-system/single-box approach to accurately predict the folding free energy change upon both conserving and charge-changing mutations. The enhanced protocol can accurately predict both types of mutations, thereby outperforming existing state-of-the-art methods in overall performance.
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Affiliation(s)
- Jason Kurniawan
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takashi Ishida
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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26
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Han Q, Tao F, Yang P. Amyloid-Like Assembly to Form Film at Interfaces: Structural Transformation and Application. Macromol Biosci 2023; 23:e2300172. [PMID: 37257459 DOI: 10.1002/mabi.202300172] [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: 04/21/2023] [Revised: 05/29/2023] [Indexed: 06/02/2023]
Abstract
Protein-based biomaterials are attracting broad interest for their remarkable structural and functional properties. Disturbing the native protein's three-dimensional structural stability in vitro and controlling subsequent aggregation is an effective strategy to design and construct protein-based biomaterials. One of the recent developments in regulating protein structural transformation to ordered aggregation is amyloid assembly, which generates fibril-based 1D to 3D nanostructures as functional materials. Especially, the amyloid-like assembly to form films at interfaces has been reported, which is induced by the effective reduction of the intramolecular disulfide bond. The main contribution of this amyloid-like assembly is the large-scale formation of protein films at interfaces and excellent adhesion to target substrates. This review presents the research progress of the amyloid-like assembly to form films and related applications and thereby provides a guide to exploiting protein-based biomaterials.
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Affiliation(s)
- Qian Han
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Fei Tao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, China
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27
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Tang Y, Zhang D, Gong X, Zheng J. Cross-seeding enables repurposing of aurein antimicrobial peptides as a promoter of human islet amyloid polypeptide (hIAPP). J Mater Chem B 2023; 11:7920-7932. [PMID: 37431688 DOI: 10.1039/d3tb01099f] [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: 07/12/2023]
Abstract
Since hIAPP (human islet amyloid polypeptide) aggregation and microbial infection are recognized as significant risk factors that contribute to the pathogenesis of type II diabetes (T2D), targeting these catastrophic processes simultaneously may have a greater impact on the prevention and treatment of T2D. Different from the well-studied hIAPP inhibitors, here we propose and demonstrate a repurposing strategy for an antimicrobial peptide, aurein, which can simultaneously modulate hIAPP aggregation and inhibit microbial infection. Collective data from protein, cell, and bacteria assays revealed multiple functions of aurein including (i) promotion of hIAPP aggregation at a low molar ratio of aurein:hIAPP = 0.5 : 1-2 : 1, (ii) reduction of hIAPP-induced cytotoxicity in RIN-m5F cells, and (iii) preservation of original antimicrobial activity against E. coli., S.A., and S.E. strains in the presence of hIAPP. These functions of aurein are mainly derived from its strong binding to different hIAPP seeds through conformationally similar β-sheet association. Our study provides a promising avenue for the repurposing of antimicrobial peptides (such as aurein) as amyloid modulators for blocking at least two pathological pathways in T2D.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA.
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA.
| | - Xiong Gong
- School of Polymer Science and Polymer Engineering, The University of Akron, Ohio, USA
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA.
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28
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Heath SL, Horne WS, Lengyel GA. Effects of chirality and side chain length in C α,α-dialkylated residues on β-hairpin peptide folded structure and stability. Org Biomol Chem 2023; 21:6320-6324. [PMID: 37503895 PMCID: PMC10445279 DOI: 10.1039/d3ob00963g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Strategic incorporation of achiral Cα,α-dialkylated amino acids with bulky substituents into peptides can be used to promote extended strand conformations and inhibit protein-protein interactions associated with amyloid formation. In this work, we evaluate the thermodynamic impact of chiral Cα,α monomers on folding preferences in such systems through introduction of a series of Cα-methylated and Cα-ethylated residues into a β-hairpin host sequence. Depending on stereochemical configuration of the artificial monomer and potential for additional hydrophobic packing, a Cα-ethyl-Cα-propyl glycine residue can provide similar or enhanced folded stability relative to an achiral Cα,α-diethyl analogue.
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Affiliation(s)
- Shelby L Heath
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - George A Lengyel
- Department of Chemistry, Slippery Rock University, Slippery Rock, PA 16057, USA.
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29
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Firdoos S, Dai R, Tahir RA, Khan ZY, Li H, Zhang J, Ni J, Quan Z, Qing H. In silico identification of novel stilbenes analogs for potential multi-targeted drugs against Alzheimer's disease. J Mol Model 2023; 29:209. [PMID: 37314512 DOI: 10.1007/s00894-023-05609-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/27/2023] [Indexed: 06/15/2023]
Abstract
CONTEXT Alzheimer's disease (AD) is a chronic progressive neurodegenerative syndrome, which adversely disturbs cognitive abilities as well as intellectual processes and frequently occurs in the elderly. Inhibition of cholinesterase is a valuable approach to upsurge acetylcholine concentrations in the brain and persuades the development of multi-targeted ligands against cholinesterases. METHODS The current study aims to determine the binding potential accompanied by antioxidant and anti-inflammatory activities of stilbenes-designed analogs against both cholinesterases (Acetylcholinesterase and butyrylcholinesterase) and neurotrophin targets for effective AD therapeutics. Docking results have shown that the WS6 compound exhibited the least binding energy - 10.1 kcal/mol with Acetylcholinesterase and - 7.8 kcal/mol with butyrylcholinesterase. The WS6 also showed a better binding potential with neurotrophin targets that are Brain-derived Neurotrophic Factor, Neurotrophin 4, Nerve Growth Factor, and Neurotrophin 3. The tested compounds particularly WS6 revealed significant antioxidant and anti-inflammatory activities through the comparative docking analysis with Fluorouracil and Melatonin as control drugs of antioxidants while Celecoxib and Anakinra as anti-inflammatory. The bioinformatics approaches including molecular docking calculations followed by the pharmacokinetics analysis and molecular dynamic simulations were accomplished to explore the capabilities of designed stilbenes as effective and potential leads. Root mean square deviation, root mean square fluctuations, and MM-GBSA calculations were performed through molecular dynamic simulations to extract the structural and residual variations and binding free energies through the 50-ns time scale.
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Affiliation(s)
- Sundas Firdoos
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, Beijing Institute of Technology (BIT), Beijing, 100081, People's Republic of China.
| | - Rongji Dai
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceutical, Beijing Institute of Technology (BIT), Beijing, 100081, People's Republic of China.
| | - Rana Adnan Tahir
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Muzaffarabad, Pakistan
| | - Zahid Younas Khan
- Department of Computer Science and IT, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Hui Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jun Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhenzhen Quan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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30
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Vanecek AS, Mojsilovic-Petrovic J, Kalb RG, Tepe JJ. Enhanced Degradation of Mutant C9ORF72-Derived Toxic Dipeptide Repeat Proteins by 20S Proteasome Activation Results in Restoration of Proteostasis and Neuroprotection. ACS Chem Neurosci 2023. [PMID: 37015082 DOI: 10.1021/acschemneuro.2c00732] [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: 04/06/2023] Open
Abstract
A hexanucleotide repeat expansion (HRE) in an intron of gene C9ORF72 is the most common cause of familial amyotrophic lateral sclerosis and frontotemporal dementia. The HRE undergoes noncanonical translation (repeat-associated non-ATG translation) resulting in the production of five distinct dipeptide repeat (DPR) proteins. Arginine-rich DPR proteins have shown to be toxic to motor neurons, and recent evidence suggests this toxicity is associated with disruption of the ubiquitin-proteasome system. Here we report the ability of known 20S proteasome activator, TCH-165, to enhance the degradation of DPR proteins and overcome proteasome impairment evoked by DPR proteins. Furthermore, the 20S activator protects rodent motor neurons from DPR protein toxicity and restores proteostasis in cortical neuron cultures. This study suggests that 20S proteasome enhancers may have therapeutic efficacy in neurodegenerative diseases that display proteostasis defects.
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Affiliation(s)
- Allison S Vanecek
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jelena Mojsilovic-Petrovic
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Robert G Kalb
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Jetze J Tepe
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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31
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Kresoja KP, Unterhuber M, Wachter R, Thiele H, Lurz P. A cardiologist's guide to machine learning in cardiovascular disease prognosis prediction. Basic Res Cardiol 2023; 118:10. [PMID: 36939941 PMCID: PMC10027799 DOI: 10.1007/s00395-023-00982-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 03/21/2023]
Abstract
A modern-day physician is faced with a vast abundance of clinical and scientific data, by far surpassing the capabilities of the human mind. Until the last decade, advances in data availability have not been accompanied by analytical approaches. The advent of machine learning (ML) algorithms might improve the interpretation of complex data and should help to translate the near endless amount of data into clinical decision-making. ML has become part of our everyday practice and might even further change modern-day medicine. It is important to acknowledge the role of ML in prognosis prediction of cardiovascular disease. The present review aims on preparing the modern physician and researcher for the challenges that ML might bring, explaining basic concepts but also caveats that might arise when using these methods. Further, a brief overview of current established classical and emerging concepts of ML disease prediction in the fields of omics, imaging and basic science is presented.
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Affiliation(s)
- Karl-Patrik Kresoja
- Department of Internal Medicine/Cardiology, Heart Center Leipzig at University of Leipzig, Struempellstr. 39, 04289, Leipzig, Germany
- Leipzig Heart Institute, Leipzig Heart Science at Heart Center Leipzig, Leipzig, Germany
| | - Matthias Unterhuber
- Department of Internal Medicine/Cardiology, Heart Center Leipzig at University of Leipzig, Struempellstr. 39, 04289, Leipzig, Germany
- Leipzig Heart Institute, Leipzig Heart Science at Heart Center Leipzig, Leipzig, Germany
| | - Rolf Wachter
- Department of Cardiology, University Hospital Leipzig, Leipzig, Germany
- Clinic for Cardiology and Pneumology, University Medicine Göttingen, Göttingen, Germany
- German Cardiovascular Research Center (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Holger Thiele
- Department of Internal Medicine/Cardiology, Heart Center Leipzig at University of Leipzig, Struempellstr. 39, 04289, Leipzig, Germany.
- Leipzig Heart Institute, Leipzig Heart Science at Heart Center Leipzig, Leipzig, Germany.
| | - Philipp Lurz
- Department of Internal Medicine/Cardiology, Heart Center Leipzig at University of Leipzig, Struempellstr. 39, 04289, Leipzig, Germany.
- Leipzig Heart Institute, Leipzig Heart Science at Heart Center Leipzig, Leipzig, Germany.
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32
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Nakama T, Rossen A, Ebihara R, Yagi-Utsumi M, Fujita D, Kato K, Sato S, Fujita M. Hysteresis behavior in the unfolding/refolding processes of a protein trapped in metallo-cages. Chem Sci 2023; 14:2910-2914. [PMID: 36937586 PMCID: PMC10016334 DOI: 10.1039/d2sc05879k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Confinement of molecules in a synthetic host can physically isolate even their unstable temporary structures, which has potential for application to protein transient structure analysis. Here we report the NMR snapshot observation of protein unfolding and refolding processes by confining a target protein in a self-assembled coordination cage. With increasing acetonitrile content in CD3CN/H2O media (50 to 90 vol%), the folding structure of a protein sharply denatured at 83 vol%, clearly revealing the regions of initial unfolding. Unfavorable aggregation of the protein leading to irreversible precipitation is completely prevented because of the spatial isolation of the single protein molecule in the cage. When the acetonitrile content reversed (84 to 70 vol%), the once-denatured protein started to regain its original folded structure at 80 vol%, showing that the protein folding/unfolding process can be referred to as a phase transition with hysteresis behavior.
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Affiliation(s)
- Takahiro Nakama
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Anouk Rossen
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Risa Ebihara
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Maho Yagi-Utsumi
- Institute for Molecular Science (IMS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya 467-8603 Japan
| | - Daishi Fujita
- Institute for Integrated Cell-Material Sciences (iCeMS), Institute for Advanced Study, Kyoto University Yoshida, Sakyo-ku Kyoto 606-8501 Japan
| | - Koichi Kato
- Institute for Molecular Science (IMS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya 467-8603 Japan
| | - Sota Sato
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Makoto Fujita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Institute for Molecular Science (IMS) 5-1 Higashiyama, Myodaiji Okazaki Aichi 444-8787 Japan
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33
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Jiang H, Li H, Wong WH, Fan X. Revealing Free Energy Landscape From MD Data via Conditional Angle Partition Tree. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1384-1394. [PMID: 35503836 DOI: 10.1109/tcbb.2022.3172352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Deciphering the free energy landscape of biomolecular structure space is crucial for understanding many complex molecular processes, such as protein-protein interaction, RNA folding, and protein folding. A major source of current dynamic structure data is Molecular Dynamics (MD) simulations. Several methods have been proposed to investigate the free energy landscape from MD data, but all of them rely on the assumption that kinetic similarity is associated with global geometric similarity, which may lead to unsatisfactory results. In this paper, we proposed a new method called Conditional Angle Partition Tree to reveal the hierarchical free energy landscape by correlating local geometric similarity with kinetic similarity. Its application on the benchmark alanine dipeptide MD data showed a much better performance than existing methods in exploring and understanding the free energy landscape. We also applied it to the MD data of Villin HP35. Our results are more reasonable on various aspects than those from other methods and very informative on the hierarchical structure of its energy landscape.
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Puneeth Kumar DRGKR, Reja RM, Senapati DK, Singh M, Nalawade SA, George G, Kaul G, Akhir A, Chopra S, Raghothama S, Gopi HN. A cationic amphiphilic peptide chaperone rescues Aβ 42 aggregation and cytotoxicity. RSC Med Chem 2023; 14:332-340. [PMID: 36846376 PMCID: PMC9945854 DOI: 10.1039/d2md00414c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
Directing Aβ42 to adopt a conformation that is free from aggregation and cell toxicity is an attractive and viable strategy to design therapeutics for Alzheimer's disease. Over the years, extensive efforts have been made to disrupt the aggregation of Aβ42 using various types of inhibitors but with limited success. Herein, we report the inhibition of aggregation of Aβ42 and disintegration of matured fibrils of Aβ42 into smaller assemblies by a 15-mer cationic amphiphilic peptide. The biophysical analysis comprising thioflavin T (ThT) mediated amyloid aggregation kinetic analysis, dynamic light scattering, ELISA, AFM, and TEM suggested that the peptide effectively disrupts Aβ42 aggregation. The circular dichroism (CD) and 2D-NMR HSQC analysis reveal that upon interaction, the peptide induces a conformational change in Aβ42 that is free from aggregation. Further, the cell assay experiments revealed that this peptide is non-toxic to cells and also rescues the cells from the toxicity of Aβ42. Peptides with a shorter length displayed either weak or no inhibitory effect on Aβ42 aggregation and cytotoxicity. These results suggest that the 15-residue cationic amphiphilic peptide reported here may serve as a potential therapeutic candidate for Alzheimer's disease.
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Affiliation(s)
- DRGKoppalu R. Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
| | - Rahi M. Reja
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
| | | | - Manjeet Singh
- Department of Chemistry, Indian Institute of Science Education and Research Dr. Homi Bhabha Road, Pashan Pune-411008 India
| | - Sachin A. Nalawade
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
| | - Gijo George
- NMR Research Centre, Indian Institute of ScienceBangalore-560012India
| | - Grace Kaul
- Division of Microbiology and Division of Medicinal and Process Chemistry, CSIR-Central Drug Research InstituteSitapur Road, Sector 10, Janakipuram ExtensionLucknow-226031Uttar PradeshIndia,AcSIR: Academy of Scientific and Innovative Research (AcSIR)Ghaziabad 201002India
| | - Abdul Akhir
- Division of Microbiology and Division of Medicinal and Process Chemistry, CSIR-Central Drug Research InstituteSitapur Road, Sector 10, Janakipuram ExtensionLucknow-226031Uttar PradeshIndia
| | - Sidharth Chopra
- Division of Microbiology and Division of Medicinal and Process Chemistry, CSIR-Central Drug Research InstituteSitapur Road, Sector 10, Janakipuram ExtensionLucknow-226031Uttar PradeshIndia,AcSIR: Academy of Scientific and Innovative Research (AcSIR)Ghaziabad 201002India
| | | | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and ResearchDr. Homi Bhabha Road, PashanPune-411008India
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35
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Puentes-Díaz N, Chaparro D, Morales-Morales D, Flores-Gaspar A, Alí-Torres J. Role of Metal Cations of Copper, Iron, and Aluminum and Multifunctional Ligands in Alzheimer's Disease: Experimental and Computational Insights. ACS OMEGA 2023; 8:4508-4526. [PMID: 36777601 PMCID: PMC9909689 DOI: 10.1021/acsomega.2c06939] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/30/2022] [Indexed: 05/15/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia, affecting millions of people around the world. Even though the causes of AD are not completely understood due to its multifactorial nature, some neuropathological hallmarks of its development have been related to the high concentration of some metal cations. These roles include the participation of these metal cations in the production of reactive oxygen species, which have been involved in neuronal damage. In order to avoid the increment in the oxidative stress, multifunctional ligands used to coordinate these metal cations have been proposed as a possible treatment to AD. In this review, we present the recent advances in experimental and computational works aiming to understand the role of two redox active and essential transition-metal cations (Cu and Fe) and one nonbiological metal (Al) and the recent proposals on the development of multifunctional ligands to stop or revert the damaging effects promoted by these metal cations.
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Affiliation(s)
- Nicolás Puentes-Díaz
- Departamento
de Química, Universidad Nacional
de Colombia−Sede Bogotá, Bogotá 11301, Colombia
| | - Diego Chaparro
- Departamento
de Química, Universidad Nacional
de Colombia−Sede Bogotá, Bogotá 11301, Colombia
- Departamento
de Química, Universidad Militar Nueva
Granada, Cajicá 250240, Colombia
| | - David Morales-Morales
- Instituto
de Química, Universidad Nacional Autónoma de México,
Circuito Exterior, Ciudad Universitaria, Ciudad de México 04510, México
| | - Areli Flores-Gaspar
- Departamento
de Química, Universidad Militar Nueva
Granada, Cajicá 250240, Colombia
- Areli Flores-Gaspar − Departamento de Química,
Universidad Militar Nueva
Granada, Cajicá, 250247, Colombia.
| | - Jorge Alí-Torres
- Departamento
de Química, Universidad Nacional
de Colombia−Sede Bogotá, Bogotá 11301, Colombia
- Jorge Alí-Torres − Departamento de Química, Universidad Nacional de
Colombia, Sede Bogotá,11301, Bogotá, Colombia.
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36
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Noll N, Groß T, Shoyama K, Beuerle F, Würthner F. Folding-Induced Promotion of Proton-Coupled Electron Transfers via Proximal Base for Light-Driven Water Oxidation. Angew Chem Int Ed Engl 2023; 62:e202217745. [PMID: 36511298 PMCID: PMC10107485 DOI: 10.1002/anie.202217745] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/14/2022]
Abstract
Proton-coupled electron-transfer (PCET) processes play a key role in biocatalytic energy conversion and storage, for example, photosynthesis or nitrogen fixation. Here, we report a series of bipyridine-containing di- to tetranuclear Ru(bda) macrocycles 2 C-4 C (bda: 2,2'-bipyridine-6,6'-dicarboxylate) to promote O-O bond formation. In photocatalytic water oxidation under neutral conditions, all complexes 2 C-4 C prevail in a folded conformation that support the water nucleophilic attack (WNA) pathway with remarkable turnover frequencies of up to 15.5 s-1 per Ru unit respectively. Single-crystal X-ray analysis revealed an increased tendency for intramolecular π-π stacking and preorganization of the proximal bases close to the active centers for the larger macrocycles. H/D kinetic isotope effect studies and electrochemical data demonstrate the key role of the proximal bipyridines as proton acceptors in lowering the activation barrier for the crucial nucleophilic attack of H2 O in the WNA mechanism.
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Affiliation(s)
- Niklas Noll
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Tobias Groß
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Kazutaka Shoyama
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074, Würzburg, Germany
| | - Florian Beuerle
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074, Würzburg, Germany.,Institut für Organische Chemie, Universität Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074, Würzburg, Germany
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37
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Hadi Ali Janvand S, Ladefoged LK, Zubrienė A, Sakalauskas A, Christiansen G, Dudutienė V, Schiøtt B, Matulis D, Smirnovas V, Otzen DE. Inhibitory effects of fluorinated benzenesulfonamides on insulin fibrillation. Int J Biol Macromol 2023; 227:590-600. [PMID: 36529223 DOI: 10.1016/j.ijbiomac.2022.12.105] [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: 08/06/2022] [Revised: 11/15/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
Amyloid fibrils are protein aggregates formed by protein assembly through cross β structures. Inhibition of amyloid fibril formation may contribute to therapy against amyloid-related disorders like Parkinson's, Alzheimer's, and type 2 diabetes. Here we report that several fluorinated sulfonamide compounds, previously shown to inhibit human carbonic anhydrase, also inhibit the fibrillation of different proteins. Using a range of spectroscopic, microscopic and chromatographic techniques, we found that the two fluorinated sulfonamide compounds completely inhibit insulin fibrillation over a period of 16 h and moderately suppress α-synuclein and Aβ fibrillation. In addition, these compounds decreased cell toxicity of insulin incubated under fibrillation-inducing conditions. We ascribe these effects to their ability to maintain insulin in the native monomeric state. Molecular dynamic simulations suggest that these compounds inhibit insulin self-association by interacting with residues at the dimer interface. This highlights the general anti-aggregative properties of aromatic sulfonamides and suggests that sulfonamide compounds which inhibit carbonic anhydrase activity may have potential as therapeutic agents against amyloid-related disorders.
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Affiliation(s)
- Saeid Hadi Ali Janvand
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Lucy Kate Ladefoged
- iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Andrius Sakalauskas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gunna Christiansen
- Department of Health Science and Technology, Medical Microbiology and Immunology, Aalborg University, Fredrik Bajers Vej 3b, DK-9220 Aalborg Ø, Denmark
| | - Virginija Dudutienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Birgit Schiøtt
- iNANO and Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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38
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Cheong DY, Roh S, Park I, Lin Y, Lee YH, Lee T, Lee SW, Lee D, Jung HG, Kim H, Lee W, Yoon DS, Hong Y, Lee G. Proteolysis-driven proliferation and rigidification of pepsin-resistant amyloid fibrils. Int J Biol Macromol 2023; 227:601-607. [PMID: 36543295 DOI: 10.1016/j.ijbiomac.2022.12.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/20/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022]
Abstract
Proteolysis of amyloids is related to prevention and treatment of amyloidosis. What if the conditions for proteolysis were the same to those for amyloid formation? For example, pepsin, a gastric protease is activated in an acidic environment, which, interestingly, is also a condition that induces the amyloid formation. Here, we investigate the competition reactions between proteolysis and synthesis of amyloid under pepsin-activated conditions. The changes in the quantities and nanomechanical properties of amyloids after pepsin treatment were examined by fluorescence assay, circular dichroism and atomic force microscopy. We found that, in the case of pepsin-resistant amyloid, a secondary reaction can be accelerated, thereby proliferating amyloids. Moreover, after this reaction, the amyloid became 32.4 % thicker and 24.2 % stiffer than the original one. Our results suggest a new insight into the proteolysis-driven proliferation and rigidification of pepsin-resistant amyloids.
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Affiliation(s)
- Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Seokbeom Roh
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Insu Park
- Department of Biomedical Engineering, Konyang University, Daejeon 35365, South Korea
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea; Research Headquarters, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Taeha Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea
| | - Sang Won Lee
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea
| | - Dongtak Lee
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea
| | - Hyo Gi Jung
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, South Korea
| | - Hyunji Kim
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, South Korea
| | - Wonseok Lee
- Department of Electrical Engineering, Korea National University of Transportation, Chungju 27469, South Korea
| | - Dae Sung Yoon
- School of Biomedical Engineering, Korea University, Seoul 02841, South Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul 02841, South Korea; ASTRION Inc., Seoul 02841, South Korea.
| | - Yoochan Hong
- Department of Medical Devices, Korea Institute of Machinery and Materials (KIMM), Daegu 42994, South Korea.
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, South Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, South Korea.
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Zein HF, Sutthibutpong T. Roles of Tryptophan and Charged Residues on the Polymorphisms of Amyloids Formed by K-Peptides of Hen Egg White Lysozyme Investigated through Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24032626. [PMID: 36768943 PMCID: PMC9916845 DOI: 10.3390/ijms24032626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/31/2023] Open
Abstract
Atomistic molecular dynamics simulations of amyloid models, consisting of the previously reported STDY-K-peptides and K-peptides from the hen egg white lysozyme (HEWL), were performed to address the effects of charged residues and pH observed in an in vitro study. Simulation results showed that amyloid models with antiparallel configurations possessed greater stability and compactness than those with parallel configurations. Then, peptide chain stretching and ordering were measured through the end-to-end distance and the order parameter, for which the amyloid models consisting of K-peptides and the STDY-K-peptides at pH 2 displayed a higher level of chain stretching and ordering. After that, the molecular mechanics energy decomposition and the radial distribution function (RDF) clearly displayed the importance of Trp62 to the K-peptide and the STDY-K-peptide models at pH 2. Moreover, the results also displayed how the negatively charged Asp52 disrupted the interaction networks and prevented the amyloid formation from STDY-K-peptide at pH 7. Finally, this study provided an insight into the interplay between pH conditions and molecular interactions underlying the formation of amyloid fibrils from short peptides contained within the HEWL. This served as a basis of understanding towards the design of other amyloids for biomaterial applications.
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Affiliation(s)
- Husnul Fuad Zein
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
- Department of Physics, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Thana Sutthibutpong
- Nanoscience and Nanotechnology Program, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
- Department of Physics, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
- Correspondence:
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40
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Maity D. Inhibition of Amyloid Protein Aggregation Using Selected Peptidomimetics. ChemMedChem 2023; 18:e202200499. [PMID: 36317359 DOI: 10.1002/cmdc.202200499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Aberrant protein aggregation leads to the formation of amyloid fibrils. This phenomenon is linked to the development of more than 40 irremediable diseases such as Alzheimer's disease, Parkinson's disease, type 2 diabetes, and cancer. Plenty of research efforts have been given to understanding the underlying mechanism of protein aggregation, associated toxicity, and the development of amyloid inhibitors. Recently, the peptidomimetic approach has emerged as a potential tool to modulate several protein-protein interactions (PPIs). In this review, we discussed selected peptidomimetic-based approaches for the modulation of important amyloid proteins (Islet Amyloid Polypeptide, Amyloid Beta, α-synuclein, mutant p53, and insulin) aggregation. This approach holds a powerful platform for creating an essential stepping stone for the vital development of anti-amyloid therapeutic agents.
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Affiliation(s)
- Debabrata Maity
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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41
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Wang Z, Wang Q, Li S, Li XJ, Yang W, He D. Microglial autophagy in Alzheimer's disease and Parkinson's disease. Front Aging Neurosci 2023; 14:1065183. [PMID: 36704504 PMCID: PMC9872664 DOI: 10.3389/fnagi.2022.1065183] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative diseases, characterized by gradual and selective loss of neurons in the central nervous system. They affect more than 50 million people worldwide, and their incidence increases with age. Although most cases of AD and PD are sporadic, some are caused by genetic mutations that are inherited. Both sporadic and familial cases display complex neuropathology and represent the most perplexing neurological disorders. Because of the undefined pathogenesis and complex clinical manifestations, there is still no effective treatment for both AD and PD. Understanding the pathogenesis of these important neurodegenerative diseases is important for developing successful therapies. Increasing evidence suggests that microglial autophagy is associated with the pathogenesis of AD and PD, and its dysfunction has been implicated in disease progression. In this review, we focus on the autophagy function in microglia and its dysfunction in AD and PD disease models in an attempt to help our understanding of the pathogenesis and identifying new therapeutic targets of AD and PD.
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Affiliation(s)
| | | | | | | | | | - Dajian He
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
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42
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Li Z, Wu H, Ji Y, Shi Z, Liu S, Bao X, Shan P, Hu D, Li M. Toward Reagent-Free Discrimination of Alzheimer's Disease Using Blood Plasma Spectral Digital Biomarkers and Machine Learning. J Alzheimers Dis 2023; 95:1175-1188. [PMID: 37661884 DOI: 10.3233/jad-230248] [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: 09/05/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most prevalent neurodegenerative disease. The detection of early-stage AD is particularly desirable because it would allow early intervention. However, a minimally invasive, low-cost, and accurate discrimination or diagnostic method for AD is especially difficult in the earliest stage of AD. OBJECTIVE The aim of this research is to discover blood plasma spectral digital biomarkers of AD, develop a novel intelligent method for the discrimination of AD and accelerate the translation of Fourier transform infrared (FTIR) spectral-based disease discrimination methods from the laboratory to clinical practice. METHODS Since vibration spectroscopy can provide the structure and chemical composition information of biological samples at the molecular level, we investigated the potential of FTIR spectral biomarkers of blood plasma to differentiate between AD patients and healthy controls. Combined with machine learning technology, we designed a hierarchical discrimination system that provides reagent-free and accurate AD discrimination based on blood plasma spectral digital biomarkers of AD. RESULTS Accurate segregation between AD patients and healthy controls was achieved with 89.3% sensitivity and 85.7% specificity for early-stage AD patients, 92.8% sensitivity and 87.5% specificity for middle-stage AD patients, and 100% sensitivity and 100% specificity for late-stage AD patients. CONCLUSIONS Our results show that blood plasma spectral digital biomarkers hold great promise as discrimination markers of AD, indicating the potential for the development of an inexpensive, reagent-free, and less laborious clinical test. As a result, our research outcome will accelerate the clinical application of spectral digital biomarkers and machine learning.
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Affiliation(s)
- Zhigang Li
- College of Information Science and Engineering, Northeastern University, Shenyang, China
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, China
| | - Hao Wu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Yong Ji
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Zhihong Shi
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Shuai Liu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Xinran Bao
- First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Peng Shan
- College of Information Science and Engineering, Northeastern University, Shenyang, China
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, China
| | - Dean Hu
- College of Information Science and Engineering, Northeastern University, Shenyang, China
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, China
| | - Meimei Li
- College of Information Science and Engineering, Northeastern University, Shenyang, China
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43
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Bo S, Sun Q, Ning P, Yuan N, Weng Y, Liang Y, Wang H, Lu Z, Li Z, Zhao X. A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA. Front Genet 2023; 14:1151172. [PMID: 36923795 PMCID: PMC10008863 DOI: 10.3389/fgene.2023.1151172] [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: 01/25/2023] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Studies have shown that post-spliced introns promote cell survival when nutrients are scarce, and intron loss/gain can influence many stages of mRNA metabolism. However, few approaches are currently available to study the correlation between intron sequences and their corresponding mature mRNA sequences. Here, based on the results of the improved Smith-Waterman local alignment-based algorithm method (SW method) and binding free energy weighted local alignment algorithm method (BFE method), the optimal matched segments between introns and their corresponding mature mRNAs in Caenorhabditis elegans (C.elegans) and their relative matching frequency (RF) distributions were obtained. The results showed that although the distributions of relative matching frequencies on mRNAs obtained by the BFE method were similar to the SW method, the interaction intensity in 5'and 3'untranslated regions (UTRs) regions was weaker than the SW method. The RF distributions in the exon-exon junction regions were comparable, the effects of long and short introns on mRNA and on the five functional sites with BFE method were similar to the SW method. However, the interaction intensity in 5'and 3'UTR regions with BFE method was weaker than with SW method. Although the matching rate and length distribution shape of the optimal matched fragment were consistent with the SW method, an increase in length was observed. The matching rates and the length of the optimal matched fragments were mainly in the range of 60%-80% and 20-30bp, respectively. Although we found that there were still matching preferences in the 5'and 3'UTR regions of the mRNAs with BFE, the matching intensities were significantly lower than the matching intensities between introns and their corresponding mRNAs with SW method. Overall, our findings suggest that the interaction between introns and mRNAs results from synergism among different types of sequences during the evolutionary process.
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Affiliation(s)
- Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Qiuying Sun
- Department of Oncology, Inner Mongolia Cancer Hospital and The Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Pengfei Ning
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Ningping Yuan
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Yujie Weng
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Ying Liang
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Huitao Wang
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.,School of Life Science, Inner Mongolia University, Hohhot, China.,Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China.,6 Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
| | - Zhongxian Li
- College of Computer Information, Inner Mongolia Medical University, Hohhot, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China.,School of Life Science, Inner Mongolia University, Hohhot, China.,Key Laboratory of Black Soil Protection And Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China.,6 Inner Mongolia Key Laboratory of Degradation Farmland Ecological Restoration and Pollution Control, Hohhot, China
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44
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Khan AN, Khan RH. Protein misfolding and related human diseases: A comprehensive review of toxicity, proteins involved, and current therapeutic strategies. Int J Biol Macromol 2022; 223:143-160. [PMID: 36356861 DOI: 10.1016/j.ijbiomac.2022.11.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Most of the cell's chemical reactions and structural components are facilitated by proteins. But proteins are highly dynamic molecules, where numerous modifications or changes in the cellular environment can affect their native conformational fold leading to protein aggregation. Various stress conditions, such as oxidative stress, mutations and metal toxicity may cause protein misfolding and aggregation by shifting the conformational equilibrium towards more aggregation-prone states. Most of the protein misfolding diseases (PMDs) involve aggregation of protein. We have discussed such proteins like Aβ peptide, α-synuclein, amylin and lysozyme involved in Alzheimer's, Parkinson's, type II diabetes and non-neuropathic systemic amyloidosis respectively. Till date, all advances in PMDs therapeutics help symptomatically but do not prevent the root cause of the disease, i.e., the aggregation of protein involved in the diseases. Current efforts focused on developing therapies for PMDs have employed diverse strategies; repositioning pre-existing drugs as it saves time and money; natural compounds that are touted as potential drug candidates have an advantage of being taken in diet normally and will induce lesser side effects. This review also covers recently developed therapeutic strategies like antisense drugs and disaggregases which has yielded therapeutic agents that have transitioned from preclinical studies into human clinical trials.
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Affiliation(s)
- Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, AMU, Aligarh 202002, India
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45
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Patel KB, Patel DV, Patel NR, Kanhed AM, Teli DM, Gandhi B, Shah BS, Chaudhary BN, Prajapati NK, Patel KV, Yadav MR. Carbazole-based semicarbazones and hydrazones as multifunctional anti-Alzheimer agents. J Biomol Struct Dyn 2022; 40:10278-10299. [PMID: 34215173 DOI: 10.1080/07391102.2021.1942212] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
With the aim to combat a multi-faceted neurodegenerative Alzheimer's disease (AD), a series of carbazole-based semicarbazide and hydrazide derivatives were designed, synthesized and assessed for their cholinesterase (ChE) inhibitory, antioxidant and biometal chelating activity. Among them, (E)-2-((9-ethyl-9H-carbazol-3-yl)methylene)-N-(pyridin-2-yl)hydrazinecarbothioamide (62) and (E)-2-((9-ethyl-9H-carbazol-3-yl)methylene)-N-(5-chloropyridin-2-yl)hydrazinecarbothioamide (63) emerged as the premier candidates with good ChE inhibitory activities (IC50 values of 1.37 µM and 1.18 µM for hAChE, IC50 values of 2.69 µM and 3.31 µM for EqBuChE, respectively). All the test compounds displayed excellent antioxidant activity (reduction percentage of DPPH values for compounds (62) and (63) were 85.67% and 84.49%, respectively at 100 µM concentration). Compounds (62) and (63) conferred specific copper ion chelating property in metal chelation study. Molecular docking studies of compounds (62) and (63) indicate strong interactions within the active sites of both the ChE enzymes. Besides that, these compounds also exhibited significant in silico drug-like pharmacokinetic properties. Thus, taken together, they can serve as a starting point in the designing of multifunctional ligands in pursuit of potential anti-AD agents that might further prevent the progression of ADs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kishan B Patel
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Dushyant V Patel
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Nirav R Patel
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Ashish M Kanhed
- Shobhaben Pratapbhai Patel - School of Pharmacy & Technology Management, SVKM's NMIMS University, Mumbai, India
| | - Divya M Teli
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Navrangpura, Gujarat, India
| | - Bhumi Gandhi
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Bhavik S Shah
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Bharat N Chaudhary
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Navnit K Prajapati
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Kirti V Patel
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Mange Ram Yadav
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India.,Centre of Research for Development, Parul University, Vadodara, Gujarat, India
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46
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Fazelinejad H, Zahedi E, Nazarian S, Kaffash Siuki Z, Nasri S, Dadmehr M, Mehrabi M, Khodarahmi R. Neuroprotective effect of Bis(Indolyl)phenylmethane in Alzheimer’s disease rat model through inhibition of hen Lysozyme amyloid fibril-induced neurotoxicity. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02692-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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47
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Pal T, Sahoo S, Prasad Ghanta K, Bandyopadhyay S. Computational Investigation of Conformational Fluctuations of Aβ42 Monomers in Aqueous Ionic Liquid Mixtures. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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An D, Ban Q, Du H, Wang Q, Teng F, Li L, Xiao H. Nanofibrils of food-grade proteins: Formation mechanism, delivery systems, and application evaluation. Compr Rev Food Sci Food Saf 2022; 21:4847-4871. [PMID: 36201382 DOI: 10.1111/1541-4337.13028] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 01/28/2023]
Abstract
Due to the high aspect ratio, appealing mechanical characteristics, and various adjustable functional groups on the surface proteins, food-grade protein nanofibrils have attracted great research interest in the field of food science. Fibrillation, known as a process of peptide self-assembly, is recognized as a common attribute for food-grade proteins. Converting food-grade proteins into nanofibrils is a promising strategy to broaden their functionality and applications, such as improvement of the properties of gelling and emulsifying, especially for constructing various delivery systems for bioactive compounds. Protein source and processing conditions have a great impact on the size, structure, and morphology of nanofibrils, resulting in extreme differences in functionality. With this feature, it is possible to engineer nanofibrils into four different delivery systems, including gels, microcapsules, emulsions, and complexes. Construction of nanofibril-based gels via multiple cross-linking methods can endow gels with special network structures to efficiently capture bioactive compounds and extra mechanical behavior. The adsorption behavior of nanofibrils at the interface is highly complex due to the influence of several intrinsic factors, which makes it challenging to form stabilized nanofibril-based emulsion systems. Based on electrostatic interactions, microcapsules and complexes prepared using nanofibrils and polysaccharides have combined functional properties, resulting in adjustable release behavior and higher encapsulation efficiency. The bioactive compounds delivery system based on nanofibrils is a potential solution to enhance their absorption in the gastrointestinal tract, improve their bioavailability, and deliver them to target organs. Although food-grade protein nanofibrils show unknown toxicity to humans, further research can contribute to broadening the application of nanofibrils in delivery systems.
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Affiliation(s)
- Di An
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Qingfeng Ban
- College of Food Science, Northeast Agricultural University, Harbin, China.,Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Hengjun Du
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Qi Wang
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Fei Teng
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Liang Li
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
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49
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Hou T, Zhang N, Yan C, Ding M, Niu H, Guan P, Hu X. Curcumin-loaded protein imprinted mesoporous nanosphere for inhibiting amyloid aggregation. Int J Biol Macromol 2022; 221:334-345. [PMID: 36084870 DOI: 10.1016/j.ijbiomac.2022.08.185] [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: 06/28/2022] [Revised: 08/18/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022]
Abstract
Some natural variants of human lysozyme are associated with systemic non-neurological amyloidosis that leads to amyloid protein fibril deposition in different tissues. Inhibition of amyloid fibrillation by nanomaterials is considered to be an effective approach to treating amyloidosis. Here, we prepared a targeted, highly loaded curcumin lysozyme-imprinted nanosphere (CUR-MIMS) that could effectively inhibit the aggregation of lysozyme with lysozyme adsorption capacity of 193.57 mg g-1 and the imprinting factor (IF) of 3.72. CUR-MIMS could bind to lysozyme through hydrophobic interactions and effectively reduce the hydrophobicity of the total solvent-exposed surface in lysozyme fibrillation, thus reducing the self-assembly process triggered by hydrophobic interactions. Thioflavin T (ThT) analysis demonstrated that CUR-MIMS inhibited the aggregation of amyloid fibrils in a dose-dependent manner (inhibition efficiency of 56.07 %). Circular dichroism (CD) spectrum further illustrated that CUR-MIMS could significantly inhibit the transition of lysozyme from α-helix structure to β-sheet. More importantly, biological experiments proved the good biocompatibility of CUR-MIMS, which indicated the potential of our system as a future therapeutic platform for amyloidosis.
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Affiliation(s)
- Tongtong Hou
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Nan Zhang
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Chaoren Yan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Minling Ding
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Huizhe Niu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China
| | - Ping Guan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China.
| | - Xiaoling Hu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an 710072, PR China.
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50
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Luttik K, Olmos V, Owens A, Khan A, Yun J, Driessen T, Lim J. Identifying Disease Signatures in the Spinocerebellar Ataxia Type 1 Mouse Cortex. Cells 2022; 11:2632. [PMID: 36078042 PMCID: PMC9454518 DOI: 10.3390/cells11172632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The neurodegenerative disease spinocerebellar ataxia type 1 (SCA1) is known to lead to the progressive degeneration of specific neuronal populations, including cerebellar Purkinje cells (PCs), brainstem cranial nerve nuclei and inferior olive nuclei, and spinocerebellar tracts. The disease-causing protein ataxin-1 is fairly ubiquitously expressed throughout the brain and spinal cord, but most studies have primarily focused on the role of ataxin-1 in the cerebellum and brainstem. Therefore, the functions of ataxin-1 and the effects of SCA1 mutations in other brain regions including the cortex are not well-known. Here, we characterized pathology in the motor cortex of a SCA1 mouse model and performed RNA sequencing in this brain region to investigate the impact of mutant ataxin-1 towards transcriptomic alterations. We identified progressive cortical pathology and significant transcriptomic changes in the motor cortex of a SCA1 mouse model. We also identified progressive, region-specific, colocalization of p62 protein with mutant ataxin-1 aggregates in broad brain regions, but not the cerebellum or brainstem. A cross-regional comparison of the SCA1 cortical and cerebellar transcriptomic changes identified both common and unique gene expression changes between the two regions, including shared synaptic dysfunction and region-specific kinase regulation. These findings suggest that the cortex is progressively impacted via both shared and region-specific mechanisms in SCA1.
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Affiliation(s)
- Kimberly Luttik
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Victor Olmos
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ashley Owens
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Joy Yun
- Yale College, New Haven, CT 06510, USA
| | - Terri Driessen
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Janghoo Lim
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06510, USA
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