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Roterman I, Slupina M, Stapor K, Konieczny L, Gądek K, Nowakowski P. Chameleon Sequences-Structural Effects in Proteins Characterized by Hydrophobicity Disorder. ACS OMEGA 2024; 9:38506-38522. [PMID: 39310170 PMCID: PMC11411663 DOI: 10.1021/acsomega.4c03658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/25/2024]
Abstract
Repeated protein folding processes both in vivo and in vitro leading to the same structure for a specific amino acid sequence prove that the amino acid sequence determines protein structuring. This is also evidenced by the variability of structuring, dependent on the introduced mutations. An important phenomenon in this regard is the presence of a differentiated secondary structure for chain fragments of identical sequence representing distinct forms of the secondary-order structure. Proteins termed chameleon proteins contain polypeptide chain fragments of identical sequence (length 6-12 aa) showing structural differentiation: helix versus β-structure. In the present paper, it was shown that these fragments represent components matching the structural status dictated by the physicochemical properties of the entire structural unit. This structural matching is related to achieving the goal of the biological function of the structural unit. The corresponding secondary structure represents a means to achieving this goal, not an end in itself. A selected set of proteins from the ChSeq database have been analyzed using a fuzzy oil drop model (FOD-M) identifying the uniqueness of the hydrophobicity distribution taken as a medium for recording the specificity of a given protein and a given chameleon section in particular. It was shown that in the vast majority, the status of chameleon sections turns out to be comparable regardless of the represented secondary structure.
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Affiliation(s)
- Irena Roterman
- Department
of Bioinformatics and Telemedicine, Jagiellonian
University—Medical College, Medyczna 7, 30-688 Krakow, Poland
| | - Mateusz Slupina
- ALSTOM
ZWUS Sp. z o.o., Modelarska
12, 40-142 Katowice, Poland
| | - Katarzyna Stapor
- Faculty
of Automatic, Electronics and Computer Science, Department of Applied
Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Leszek Konieczny
- Chair
of Medical Biochemistry, Jagiellonian University—Medical
College, Kopernika 7, 31-034 Krakow, Poland
| | - Krzysztof Gądek
- AGH
Cyfronet, SANO SCIENCE, Nawojki 11, 30-950 Kraków, Poland
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2
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Bhopatkar AA, Bhatt N, Haque MA, Xavier R, Fung L, Jerez C, Kayed R. MAPT mutations associated with familial tauopathies lead to formation of conformationally distinct oligomers that have cross-seeding ability. Protein Sci 2024; 33:e5099. [PMID: 39145409 PMCID: PMC11325167 DOI: 10.1002/pro.5099] [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: 04/21/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 08/16/2024]
Abstract
The microtubule associated protein, tau, is implicated in a multitude of neurodegenerative disorders that are collectively termed as tauopathies. These disorders are characterized by the presence of tau aggregates within the brain of afflicted individuals. Mutations within the MAPT gene that encodes the tau protein form the genetic backdrop for familial forms of tauopathies, such as frontotemporal dementia (FTD), but the molecular consequences of such alterations and their pathological effects are unclear. We sought to investigate the conformational properties of the aggregates of three tau mutants: A152T, P301L, and R406W, all implicated within FTD, and compare them to those of the native form (WT-Tau 2N4R). Our immunochemical analysis reveals that mutants and WT tau oligomers exhibit similar affinity for conformation-specific antibodies but have distinct morphology and secondary structure. Additionally, these oligomers possess different dye-binding properties and varying sensitivity to proteolytic processing. These results point to conformational variety among them. We then tested the ability of the mutant oligomers to cross-seed the aggregation of WT tau monomer. Using similar array of experiments, we found that cross-seeding with mutant aggregates leads to the formation of conformationally unique WT oligomers. The results discussed in this paper provide a novel perspective on the structural properties of oligomeric forms of WT tau 2N4R and its mutant, along with shedding some light on their cross-seeding behavior.
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Affiliation(s)
- Anukool A. Bhopatkar
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
- Present address:
Department of Pharmacology and ToxicologyUniversity of Mississippi Medical CenterJacksonMississippiUSA
| | - Nemil Bhatt
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Md Anzarul Haque
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Rhea Xavier
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Leiana Fung
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
- Present address:
Neuroscience Graduate Program, UT Southwestern Medical CenterDallasTexasUSA
| | - Cynthia Jerez
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Rakez Kayed
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
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Choi ES, Hnath B, Sha CM, Dokholyan NV. Unveiling the double-edged sword: SOD1 trimers possess tissue-selective toxicity and bind septin-7 in motor neuron-like cells. Structure 2024:S0969-2126(24)00319-8. [PMID: 39208794 DOI: 10.1016/j.str.2024.08.002] [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: 04/11/2024] [Revised: 06/10/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024]
Abstract
Misfolded species of superoxide dismutase 1 (SOD1) are associated with increased death in amyotrophic lateral sclerosis (ALS) models compared to insoluble protein aggregates. The mechanism by which structurally independent SOD1 trimers cause cellular toxicity is unknown but may drive disease pathology. Here, we uncovered the SOD1 trimer interactome-a map of potential tissue-selective protein-binding partners in the brain, spinal cord, and skeletal muscle. We identified binding partners and key pathways associated with SOD1 trimers and found that trimers may affect normal cellular functions such as dendritic spine morphogenesis and synaptic function in the central nervous system and cellular metabolism in skeletal muscle. We discovered SOD1 trimer-selective enrichment of genes. We performed detailed computational and biochemical characterization of SOD1 trimer protein binding for septin-7. Our investigation highlights key proteins and pathways within distinct tissues, revealing a plausible intersection of genetic and pathophysiological mechanisms in ALS through interactions involving SOD1 trimers.
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Affiliation(s)
- Esther Sue Choi
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA, USA
| | - Brianna Hnath
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Penn State University, University Park, PA, USA
| | - Congzhou Mike Sha
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Penn State University, University Park, PA, USA; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA; Department of Chemistry, Penn State University, University Park, PA, USA.
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4
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Lee T, Cheong DY, Lee KH, You JH, Park J, Lee G. Capillary Flow-Based One-Minute Quantification of Amyloid Proteolysis. BIOSENSORS 2024; 14:400. [PMID: 39194629 DOI: 10.3390/bios14080400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Quantifying the formation and decomposition of amyloid is a crucial issue in the development of new drugs and therapies for treating amyloidosis. The current technologies for grasping amyloid formation and decomposition include fluorescence analysis using thioflavin-T, secondary structure analysis using circular dichroism, and image analysis using atomic force microscopy or transmission electron microscopy. These technologies typically require spectroscopic devices or expensive nanoscale imaging equipment and involve lengthy analysis, which limits the rapid screening of amyloid-degrading drugs. In this study, we introduce a technology for rapidly assessing amyloid decomposition using capillary flow-based paper (CFP). Amyloid solutions exhibit gel-like physical properties due to insoluble denatured polymers, resulting in a shorter flow distance on CFP compared to pure water. Experimental conditions were established to consistently control the flow distance based on a hen-egg-white lysozyme amyloid solution. It was confirmed that as amyloid is decomposed by trypsin, the flow distance increases on the CFP. Our method is highly useful for detecting changes in the gel properties of amyloid solutions within a minute, and we anticipate its use in the rapid, large-scale screening of anti-amyloid agents in the future.
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Affiliation(s)
- Taeha Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, Republic of Korea
| | - Da Yeon Cheong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, Republic of Korea
| | - Kang Hyun Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Hyun You
- Department of Digital Management, Korea University, Sejong 30019, Republic of Korea
| | - Jinsung Park
- Department of Biomechatronic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of MetaBioHealth, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
- Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong 30019, Republic of Korea
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Martins G, Galamba N. Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study. J Chem Inf Model 2024; 64:6115-6131. [PMID: 39046235 PMCID: PMC11323248 DOI: 10.1021/acs.jcim.4c00965] [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: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
Abstract
α-Synuclein (α-syn) is a 140 amino acid intrinsically disordered protein (IDP) and the primary component of cytotoxic oligomers implicated in the etiology of Parkinson's disease (PD). While IDPs lack a stable three-dimensional structure, they sample a heterogeneous ensemble of conformations that can, in principle, be assessed through molecular dynamics simulations. However, describing the structure and aggregation of large IDPs is challenging due to force field (FF) accuracy and sampling limitations. To cope with the latter, coarse-grained (CG) FFs emerge as a potential alternative at the expense of atomic detail loss. Whereas CG models can accurately describe the structure of the monomer, less is known about aggregation. The latter is key for assessing aggregation pathways and designing aggregation inhibitor drugs. Herein, we investigate the structure and dynamics of α-syn using different resolution CG (Martini3 and Sirah2) and all-atom (Amber99sb and Charmm36m) FFs to gain insight into the differences and resemblances between these models. The dependence of the magnitude of protein-water interactions and the putative need for enhanced sampling (replica exchange) methods in CG simulations are analyzed to distinguish between force field accuracy and sampling limitations. The stability of the CG models of an α-syn fibril was also investigated. Additionally, α-syn aggregation was studied through umbrella sampling for the CG models and CG/all-atom models for an 11-mer peptide (NACore) from an amyloidogenic domain of α-syn. Our results show that despite the α-syn structures of Martini3 and Sirah2 with enhanced protein-water interactions being similar, major differences exist concerning aggregation. The Martini3 fibril is not stable, and the binding free energy of α-syn and NACore is positive, opposite to Sirah2. Sirah2 peptides in a zwitterionic form, in turn, display termini interactions that are too strong, resulting in end-to-end orientation. Sirah2, with enhanced protein-water interactions and neutral termini, provides, however, a peptide aggregation free energy profile similar to that found with all-atom models. Overall, we find that Sirah2 with enhanced protein-water interactions is suitable for studying protein-protein and protein-drug aggregation.
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Affiliation(s)
- Gabriel
F. Martins
- BioISI—Biosystems
and Integrative Sciences Institute, Faculty
of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - Nuno Galamba
- BioISI—Biosystems
and Integrative Sciences Institute, Faculty
of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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Zampar S, Di Gregorio SE, Grimmer G, Watts JC, Ingelsson M. "Prion-like" seeding and propagation of oligomeric protein assemblies in neurodegenerative disorders. Front Neurosci 2024; 18:1436262. [PMID: 39161653 PMCID: PMC11330897 DOI: 10.3389/fnins.2024.1436262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024] Open
Abstract
Intra- or extracellular aggregates of proteins are central pathogenic features in most neurodegenerative disorders. The accumulation of such proteins in diseased brains is believed to be the end-stage of a stepwise aggregation of misfolded monomers to insoluble cross-β fibrils via a series of differently sized soluble oligomers/protofibrils. Several studies have shown how α-synuclein, amyloid-β, tau and other amyloidogenic proteins can act as nucleating particles and thereby share properties with misfolded forms, or strains, of the prion protein. Although the roles of different protein assemblies in the respective aggregation cascades remain unclear, oligomers/protofibrils are considered key pathogenic species. Numerous observations have demonstrated their neurotoxic effects and a growing number of studies have indicated that they also possess seeding properties, enabling their propagation within cellular networks in the nervous system. The seeding behavior of oligomers differs between the proteins and is also affected by various factors, such as size, shape and epitope presentation. Here, we are providing an overview of the current state of knowledge with respect to the "prion-like" behavior of soluble oligomers for several of the amyloidogenic proteins involved in neurodegenerative diseases. In addition to providing new insight into pathogenic mechanisms, research in this field is leading to novel diagnostic and therapeutic opportunities for neurodegenerative diseases.
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Affiliation(s)
- Silvia Zampar
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Sonja E. Di Gregorio
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Gustavo Grimmer
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Joel C. Watts
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Martin Ingelsson
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Public Health/Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Lippi A, Krisko A. Protein aggregation: A detrimental symptom or an adaptation mechanism? J Neurochem 2024; 168:1426-1441. [PMID: 37694504 DOI: 10.1111/jnc.15955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
Protein quality control mechanisms oversee numerous aspects of protein lifetime. From the point of protein synthesis, protein homeostasis machineries take part in folding, solubilization, and/or degradation of impaired proteins. Some proteins follow an alternative path upon loss of their solubility, thus are secluded from the cytosol and form protein aggregates. Protein aggregates differ in their function and composition, rendering protein aggregation a complex phenomenon that continues to receive plenty of attention in the scientific and medical communities. Traditionally, protein aggregates have been associated with aging and a large spectrum of protein folding diseases, such as neurodegenerative diseases, type 2 diabetes, or cataract. However, a body of evidence suggests that they may act as an adaptive mechanism to overcome transient stressful conditions, serving as a sink for the removal of misfolded proteins from the cytosol or storage compartments for machineries required upon stress release. In this review, we present examples and evidence elaborating different possible roles of protein aggregation and discuss their potential roles in stress survival, aging, and disease, as well as possible anti-aggregation interventions.
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Affiliation(s)
- Alice Lippi
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Anita Krisko
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
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Lu Z, Yu X, Li P, Wang Y, Deng Y, Li X, Wang C, Yu S. Correlations of erythrocytic oligomer α-synuclein levels with age, sex and clinical variables in patients with Parkinson's disease. Front Aging Neurosci 2024; 16:1437622. [PMID: 39144258 PMCID: PMC11322579 DOI: 10.3389/fnagi.2024.1437622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
Introduction Oligomeric alpha-synuclein in red blood cells (RBC-o-α-Syn) has been shown to be increased in patients with Parkinson's disease (PD). However, factors that affect RBC-o-α-Syn levels remain to be elucidated. The aim of this study is to analyze the correlations between RBC-o-α-Syn levels and the age, sex and different clinical variables of patients with PD. Methods 167 patients with PD and 119 healthy controls (HC) were enrolled in this study. The patients with PD were diagnosed based on the MDS clinical diagnostic criteria for PD. All participants were evaluated for their clinical characteristics. Western blot analysis was used to examine the molecular sizes of RBC-o-α-Syn. A newly established chemiluminescent immunoassay was used to measure RBC-o-α-Syn levels. Results Higher RBC-o-α-Syn levels were detected in PD patients than in HC subjects. The receiver operating characteristic (ROC) curve indicated that a cut off value of 55.29 ng/mg discriminated well between PD patients and HC subjects, with a sensitivity of 67.66% (95% CI: 60.24-74.29%), a specificity of 88.24% (95% CI: 81.22-92.86%), and an area under the curve (AUC) of 0.857. The levels of RBC-o-α-Syn were higher in female than male patients (p = 0.033). For different subtypes, the levels of RBC-o-α-Syn were higher in the MIX subtype than the tremor-dominant (TD) PD. In addition, the levels of RBC-o-α-Syn were higher in patients with than without cognitive impairment (p = 0.016), and negatively correlated with Mini-Mental State Examination (MMSE) scores (r = -0.156, p = 0.044). Conclusion Our study demonstrates that RBC-o-α-Syn levels in patients with PD are higher than those in HC subjects and affected by the sex and the severity of cognitive impairment.
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Affiliation(s)
- Zhe Lu
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xiaohan Yu
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Pengjie Li
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yiming Wang
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yeyun Deng
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xin Li
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Chaodong Wang
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Shun Yu
- Department of Neurobiology and National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
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Gatzemeier LM, Meyer F, Outeiro TF. Synthesis and Semi-Synthesis of Alpha-Synuclein: Insight into the Chemical Complexity of Synucleinopathies. Chembiochem 2024:e202400253. [PMID: 38965889 DOI: 10.1002/cbic.202400253] [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: 03/19/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/06/2024]
Abstract
The chemical rules governing protein folding have intrigued generations of researchers for decades. With the advent of artificial intelligence (AI), prediction of protein structure has improved tremendously. However, there is still a level of analysis that is only possible through wet laboratory experiments, especially in respect to the investigation of the pathological effect of mutations and posttranslational modifications (PTMs) on proteins of interest. This requires the availability of pure peptides and proteins in sufficient quantities for biophysical, biochemical, and functional studies. In this context, chemical protein synthesis and semi-synthesis are powerful tools in protein research, which help to enlighten the role of protein modification in the physiology and pathology of proteins. A protein of high interest in the field of biomedicine is alpha-synuclein (aSyn), a protein deeply associated with several devastating neurodegenerative disorders such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), or multiple systems atrophy (MSA). Here, we describe several methods and pathways to synthesize native or modified aSyn, and discuss how these approaches enable us to address pathological mechanisms that may open novel perspectives for therapeutic intervention.
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Affiliation(s)
- Luisa Maria Gatzemeier
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany
| | - Franc Meyer
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstraße 4, 37077, Göttingen, Germany
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Straße 3, 37075, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, United Kingdom
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Von Siebold-Straße 3a, 37075, Göttingen, Germany
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10
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Koroleva ON, Kuzmina NV, Dubrovin EV, Drutsa VL. Atomic force microscopy of spherical intermediates on the pathway to fibril formation of influenza A virus nuclear export protein. Microsc Res Tech 2024; 87:1131-1145. [PMID: 38270267 DOI: 10.1002/jemt.24499] [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: 08/25/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/26/2024]
Abstract
The nuclear export protein of the influenza A virus (NEP) is involved in many important processes of the virus life cycle. This makes it an attractive target for the treatment of a disease caused by a virus. Previously it has been shown, that recombinant variants of NEP are highly prone to aggregation in solution under various conditions with the formation of amyloid-like aggregates. In the present work, the amyloid nature of NEP aggregates was evidenced by Congo red binding assays. Atomic force microscopy has shown that NEP can form two types of spherical nanoparticles, which provide an alternative pathway for the formation of amyloid-like fibrils. Type I of these "fibrillogenic" spheres, formed under physiological conditions, represents the micelle-like particles with height 10-60 nm, which can generate worm-like flexible fibrils with the diameter 2.5-4.0 nm, length 20-500 nm and the Young's modulus ~73 MPa. Type II spherical aggregates with size of about 400-1000 nm, formed at elevated temperatures, includes fractions of drop-like and vesicle-like particles, generating more rigid amyloid-like fibrils with height of ~8 nm, and length of up to 2 μm. The hypothetical mechanism of fibril formation via nanospherical structures was suggested. RESEARCH HIGHLIGHTS: AFM has revealed two types of the influenza A virus nuclear export protein spherical aggregates. They provide an alternative pathway for the formation of amyloid-like fibrils. The mechanism of fibril formation via spherical structures is suggested.
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Affiliation(s)
- Olga N Koroleva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia V Kuzmina
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Evgeniy V Dubrovin
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russian Federation
- National University of Science and Technology, MISIS, Moscow, Russian Federation
| | - Valeriy L Drutsa
- A.N.Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
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Caneus J, Autar K, Akanda N, Grillo M, Long C, Jackson M, Lindquist S, Guo X, Morgan D, Hickman JJ. Validation of a functional human AD model with four AD therapeutics utilizing patterned iPSC-derived cortical neurons integrated with microelectrode arrays. RESEARCH SQUARE 2024:rs.3.rs-4313679. [PMID: 38826367 PMCID: PMC11142300 DOI: 10.21203/rs.3.rs-4313679/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Preclinical methods are needed for screening potential Alzheimer's disease (AD) therapeutics that recapitulate phenotypes found in the Mild Cognitive Impairment (MCI) stage or even before this stage of the disease. This would require a phenotypic system that reproduces cognitive deficits without significant neuronal cell death to mimic the clinical manifestations of AD during these stages. A potential functional parameter to be monitored is long-term potentiation (LTP), which is a correlate of learning and memory, that would be one of the first functions effected by AD onset. Mature human iPSC-derived cortical neurons and primary astrocytes were co-cultured on microelectrode arrays (MEA) where surface chemistry was utilized to create circuit patterns connecting two adjacent electrodes to model LTP function. LTP maintenance was significantly reduced in the presence of Amyloid-Beta 42 (Aβ42) oligomers compared to the controls, however, co-treatment with AD therapeutics (Donepezil, Memantine, Rolipram and Saracatinib) corrected Aβ42 induced LTP impairment. The results presented here illustrate the significance of the system as a validated platform that can be utilized to model and study MCI AD pathology, and potentially for the pre-MCI phase before the occurrence of significant cell death. It also has the potential to become an ideal platform for high content therapeutic screening for other neurodegenerative diseases.
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Pirhaghi M, Mamashli F, Moosavi-Movahedi F, Arghavani P, Amiri A, Davaeil B, Mohammad-Zaheri M, Mousavi-Jarrahi Z, Sharma D, Langel Ü, Otzen DE, Saboury AA. Cell-Penetrating Peptides: Promising Therapeutics and Drug-Delivery Systems for Neurodegenerative Diseases. Mol Pharm 2024; 21:2097-2117. [PMID: 38440998 DOI: 10.1021/acs.molpharmaceut.3c01167] [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: 03/06/2024]
Abstract
Currently, one of the most significant and rapidly growing unmet medical challenges is the treatment of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). This challenge encompasses the imperative development of efficacious therapeutic agents and overcoming the intricacies of the blood-brain barrier for successful drug delivery. Here we focus on the delivery aspect with particular emphasis on cell-penetrating peptides (CPPs), widely used in basic and translational research as they enhance drug delivery to challenging targets such as tissue and cellular compartments and thus increase therapeutic efficacy. The combination of CPPs with nanomaterials such as nanoparticles (NPs) improves the performance, accuracy, and stability of drug delivery and enables higher drug loads. Our review presents and discusses research that utilizes CPPs, either alone or in conjugation with NPs, to mitigate the pathogenic effects of neurodegenerative diseases with particular reference to AD and PD.
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Affiliation(s)
- Mitra Pirhaghi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 6673145137, Iran
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Fatemeh Mamashli
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | | | - Payam Arghavani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Ahmad Amiri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Bagher Davaeil
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Mahya Mohammad-Zaheri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Zahra Mousavi-Jarrahi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Ülo Langel
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C 1592-224, Denmark
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
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13
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Abioye A, Akintade D, Mitchell J, Olorode S, Adejare A. Nonintuitive Immunogenicity and Plasticity of Alpha-Synuclein Conformers: A Paradigm for Smart Delivery of Neuro-Immunotherapeutics. Pharmaceutics 2024; 16:609. [PMID: 38794271 PMCID: PMC11124533 DOI: 10.3390/pharmaceutics16050609] [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: 03/30/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Despite the extensive research successes and continuous developments in modern medicine in terms of diagnosis, prevention, and treatment, the lack of clinically useful disease-modifying drugs or immunotherapeutic agents that can successfully treat or prevent neurodegenerative diseases is an ongoing challenge. To date, only one of the 244 drugs in clinical trials for the treatment of neurodegenerative diseases has been approved in the past decade, indicating a failure rate of 99.6%. In corollary, the approved monoclonal antibody did not demonstrate significant cognitive benefits. Thus, the prevalence of neurodegenerative diseases is increasing rapidly. Therefore, there is an urgent need for creative approaches to identifying and testing biomarkers for better diagnosis, prevention, and disease-modifying strategies for the treatment of neurodegenerative diseases. Overexpression of the endogenous α-synuclein has been identified as the driving force for the formation of the pathogenic α-synuclein (α-Syn) conformers, resulting in neuroinflammation, hypersensitivity, endogenous homeostatic responses, oxidative dysfunction, and degeneration of dopaminergic neurons in Parkinson's disease (PD). However, the conformational plasticity of α-Syn proffers that a certain level of α-Syn is essential for the survival of neurons. Thus, it exerts both neuroprotective and neurotoxic (regulatory) functions on neighboring neuronal cells. Furthermore, the aberrant metastable α-Syn conformers may be subtle and difficult to detect but may trigger cellular and molecular events including immune responses. It is well documented in literature that the misfolded α-Syn and its conformers that are released into the extracellular space from damaged or dead neurons trigger the innate and adaptive immune responses in PD. Thus, in this review, we discuss the nonintuitive plasticity and immunogenicity of the α-Syn conformers in the brain immune cells and their physiological and pathological consequences on the neuroimmune responses including neuroinflammation, homeostatic remodeling, and cell-specific interactions that promote neuroprotection in PD. We also critically reviewed the novel strategies for immunotherapeutic delivery interventions in PD pathogenesis including immunotherapeutic targets and potential nanoparticle-based smart drug delivery systems. It is envisioned that a greater understanding of the nonintuitive immunogenicity of aberrant α-Syn conformers in the brain's microenvironment would provide a platform for identifying valid therapeutic targets and developing smart brain delivery systems for clinically effective disease-modifying immunotherapeutics that can aid in the prevention and treatment of PD in the future.
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Affiliation(s)
- Amos Abioye
- College of Pharmacy and Health Sciences, Belmont University, Nashville, TN 37212, USA
| | - Damilare Akintade
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - James Mitchell
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - Simisade Olorode
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - Adeboye Adejare
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph’s University, Philadelphia, PA 19131, USA;
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14
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Kumar N, Khatua P, Sinha SK. Can local heating and molecular crowders disintegrate amyloid aggregates? Chem Sci 2024; 15:6095-6105. [PMID: 38665536 PMCID: PMC11040654 DOI: 10.1039/d4sc00103f] [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: 01/06/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
The present study employs a blend of molecular dynamics simulations and a theoretical model to explore the potential disintegration mechanism of a matured Aβ octamer, aiming to offer a strategy to combat Alzheimer's disease. We investigate local heating and crowding effects on Aβ disintegration by selectively heating key Aβ segments and varying the concentration of sodium dodecyl sulphate (SDS), respectively. Despite initiation of disruption, Aβ aggregates resist complete disintegration during local heating due to rapid thermal energy distribution to the surrounding water. Conversely, although SDS molecules effectively inhibit Aβ aggregation at higher concentration through micelle formation, they fail to completely disintegrate the aggregate due to the exceedingly high energy barrier. To address the sampling challenge posed by the formidable energy barrier, we have performed well-tempered metadynamics simulations. Simulations reveal a multi-step disintegration mechanism for the Aβ octamer, suggesting a probable sequence: octamer → pentamer/hexamer ⇌ tetramer → monomer, with a rate-determining step constituting 45 kJ mol-1 barrier during the octamer to pentamer/hexamer transition. Additionally, we have proposed a novel two-state mean-field model based on Ising spins that offers an insight into the kinetics of the Aβ growth process and external perturbation effects on disintegration. Thus, the current simulation study, coupled with the newly introduced mean-field model, offers an insight into the detailed mechanisms underlying the Aβ aggregation process, guiding potential strategies for effective disintegration of Aβ aggregates.
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Affiliation(s)
- Naresh Kumar
- Department of Chemistry, Theoretical and Computational Biophysical Chemistry Group, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India +91-01881-232066
| | - Prabir Khatua
- Department of Chemistry, GITAM School of Science, GITAM (Deemed to be University) Bengaluru 562163 India
| | - Sudipta Kumar Sinha
- Department of Chemistry, Theoretical and Computational Biophysical Chemistry Group, Indian Institute of Technology Ropar Rupnagar Punjab 140001 India +91-01881-232066
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15
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Zhang DY, Wang J, Huang G, Langberg S, Ding F, Dokholyan NV. APOE regulates the transport of GM1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587789. [PMID: 38617316 PMCID: PMC11014540 DOI: 10.1101/2024.04.02.587789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Apolipoprotein E (APOE) is responsible for lipid transport, including cholesterol transport and clearance. While the ε4 allele of APOE (APOE4) is associated with a significant genetic risk factor for late-onset Alzheimer's disease (AD), no mechanistic understanding of its contribution to AD etiology has been established yet. In addition to cholesterol, monosialotetrahexosylganglioside (GM1) is a crucial lipid component in cell membranes and has been implicated in promoting the aggregation of amyloid beta protein (Aβ), a key protein associated with AD. Here, we ask whether there are direct interactions between APOE and GM1 that further impact AD pathology. We find that both APOE3 and APOE4 exhibit superior binding affinity to GM1 compared to cholesterol and have an enhanced cellular uptake to GM1 lipid structures than cholesterol lipid structures. APOE regulates the transport process of GM1 depending on the cell type, which is influenced by the expression of APOE receptors in different cell lines and alters GM1 contents in cell membranes. We also find that the presence of GM1 alters the secondary structure of APOE3 and APOE4 and enhances the binding affinity between APOE and its receptor low-density lipoprotein receptor (LDLR), consequently promoting the cellular uptake of lipid structures in the presence of APOE. To understand the enhanced cellular uptake observed in lipid structures containing 20% GM1, we determined the distribution of GM1 on the membrane and found that GM1 clustering in lipid rafts, thereby supporting the physiological interaction between APOE and GM1. Overall, we find that APOE plays a regulatory role in GM1 transport, and the presence of GM1 on the lipid structures influences this transport process. Our studies introduce a plausible direct link between APOE and AD etiology, wherein APOE regulates GM1, which, in turn, promotes Aβ oligomerization and aggregation.
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16
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Jain SK, Stevens CM, Margret JJ, Levine SN. Alzheimer's Disease: A Review of Pathology, Current Treatments, and the Potential Therapeutic Effect of Decreasing Oxidative Stress by Combined Vitamin D and l-Cysteine Supplementation. Antioxid Redox Signal 2024; 40:663-678. [PMID: 37756366 PMCID: PMC11001507 DOI: 10.1089/ars.2023.0245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023]
Abstract
Significance: Excess oxidative stress and neuroinflammation are risk factors in the onset and progression of Alzheimer's disease (AD) and its association with amyloid-β plaque accumulation. Oxidative stress impairs acetylcholine (ACH) and N-methyl-d-aspartate receptor signaling in brain areas that function in memory and learning. Glutathione (GSH) antioxidant depletion positively correlates with the cognitive decline in AD subjects. Treatments that upregulate GSH and ACH levels, which simultaneously decrease oxidative stress and inflammation, may be beneficial for AD. Recent Advances: Some clinical trials have shown a benefit of monotherapy with vitamin D (VD), whose deficiency is linked to AD or with l-cysteine (LC), a precursor of GSH biosynthesis, in reducing mild cognitive impairment. Animal studies have shown a simultaneous decrease in ACH esterase (AChE) and increase in GSH; combined supplementation with VD and LC results in a greater decrease in oxidative stress and inflammation, and increase in GSH levels compared with monotherapy with VD or LC. Therefore, cosupplementation with VD and LC has the potential of increasing GSH, downregulation of oxidative stress, and decreased inflammation and AChE levels. Future Directions: Clinical trials are needed to determine whether safe low-cost dietary supplements, using combined VD+LC, have the potential to alleviate elevated AChE, oxidative stress, and inflammation levels, thereby halting the onset of AD. Goal of Review: The goal of this review is to highlight the pathological hallmarks and current Food and Drug Administration-approved treatments for AD, and discuss the potential therapeutic effect that cosupplementation with VD+LC could manifest by increasing GSH levels in patients. Antioxid. Redox Signal. 40, 663-678.
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Affiliation(s)
- Sushil K. Jain
- Department of Pediatrics and Medicine, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
| | - Christopher M. Stevens
- Department of Pediatrics and Medicine, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
| | - Jeffrey Justin Margret
- Department of Pediatrics and Medicine, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
| | - Steven N. Levine
- Department of Pediatrics and Medicine, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, USA
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17
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Park S, Laskow TC, Chen J, Guha P, Dawn B, Kim D. Microphysiological systems for human aging research. Aging Cell 2024; 23:e14070. [PMID: 38180277 PMCID: PMC10928588 DOI: 10.1111/acel.14070] [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: 06/30/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Recent advances in microphysiological systems (MPS), also known as organs-on-a-chip (OoC), enable the recapitulation of more complex organ and tissue functions on a smaller scale in vitro. MPS therefore provide the potential to better understand human diseases and physiology. To date, numerous MPS platforms have been developed for various tissues and organs, including the heart, liver, kidney, blood vessels, muscle, and adipose tissue. However, only a few studies have explored using MPS platforms to unravel the effects of aging on human physiology and the pathogenesis of age-related diseases. Age is one of the risk factors for many diseases, and enormous interest has been devoted to aging research. As such, a human MPS aging model could provide a more predictive tool to understand the molecular and cellular mechanisms underlying human aging and age-related diseases. These models can also be used to evaluate preclinical drugs for age-related diseases and translate them into clinical settings. Here, we provide a review on the application of MPS in aging research. First, we offer an overview of the molecular, cellular, and physiological changes with age in several tissues or organs. Next, we discuss previous aging models and the current state of MPS for studying human aging and age-related conditions. Lastly, we address the limitations of current MPS and present future directions on the potential of MPS platforms for human aging research.
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Affiliation(s)
- Seungman Park
- Department of Mechanical EngineeringUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Thomas C. Laskow
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jingchun Chen
- Nevada Institute of Personalized MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Prasun Guha
- Nevada Institute of Personalized MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
- School of Life SciencesUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Buddhadeb Dawn
- Department of Internal Medicine, Kirk Kerkorian School of MedicineUniversity of Nevada, Las VegasLas VegasNevadaUSA
| | - Deok‐Ho Kim
- Department of MedicineJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
- Center for Microphysiological SystemsJohns Hopkins UniversityBaltimoreMarylandUSA
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18
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Nutini A. Amyloid oligomers and their membrane toxicity - A perspective study. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 187:9-20. [PMID: 38211711 DOI: 10.1016/j.pbiomolbio.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/21/2023] [Accepted: 01/07/2024] [Indexed: 01/13/2024]
Abstract
Amyloidosis is a condition involving a disparate group of pathologies characterized by the extracellular deposition of insoluble fibrils composed of broken-down proteins. These proteins can accumulate locally, causing peculiar symptoms, or in a widespread way, involving many organs and. causing severe systemic failure. The damage that is created is related not only to the accumulation of. amyloid fibrils but above all to the precursor oligomers of the fibrils that manage to enter the cell in a very particular way. This article analyzes the current state of research related to the entry of these oligomers into the cell membrane and the theories related to their toxicity. The paper proposed here not only aims to review the contents in the literature but also proposes a new vision of amyloid toxicity. that could occur in a multiphase process catalyzed by the cell membrane itself. In this process, the denaturation of the lipid bilayer is followed by the stabilization of a pore through energetically favorable self-assembly processes which are achieved through particular oligomeric structures.
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Affiliation(s)
- Alessandro Nutini
- Biology and Biomechanics Dept - Centro Studi Attività Motorie, Italy.
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19
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Bender SWB, Dreisler MW, Zhang M, Kæstel-Hansen J, Hatzakis NS. SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis. Nat Commun 2024; 15:1763. [PMID: 38409214 PMCID: PMC10897458 DOI: 10.1038/s41467-024-46106-0] [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: 05/10/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
The morphology of protein assemblies impacts their behaviour and contributes to beneficial and aberrant cellular responses. While single-molecule localization microscopy provides the required spatial resolution to investigate these assemblies, the lack of universal robust analytical tools to extract and quantify underlying structures limits this powerful technique. Here we present SEMORE, a semi-automatic machine learning framework for universal, system- and input-dependent, analysis of super-resolution data. SEMORE implements a multi-layered density-based clustering module to dissect biological assemblies and a morphology fingerprinting module for quantification by multiple geometric and kinetics-based descriptors. We demonstrate SEMORE on simulations and diverse raw super-resolution data: time-resolved insulin aggregates, and published data of dSTORM imaging of nuclear pore complexes, fibroblast growth receptor 1, sptPALM of Syntaxin 1a and dynamic live-cell PALM of ryanodine receptors. SEMORE extracts and quantifies all protein assemblies, their temporal morphology evolution and provides quantitative insights, e.g. classification of heterogeneous insulin aggregation pathways and NPC geometry in minutes. SEMORE is a general analysis platform for super-resolution data, and being a time-aware framework can also support the rise of 4D super-resolution data.
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Affiliation(s)
- Steen W B Bender
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Marcus W Dreisler
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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20
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Qais FA, Parveen N, Afzal M, Furkan M, Khan RH. Preventing amyloid-β oligomerization and aggregation with berberine: Investigating the mechanism of action through computational methods. Int J Biol Macromol 2024; 258:128900. [PMID: 38128802 DOI: 10.1016/j.ijbiomac.2023.128900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Neurological disorders (NDs) have become a major cause of both cognitive and physical disabilities worldwide. In NDs, misfolded proteins tend to adopt a β-sheet-rich fibrillar structure called amyloid. Amyloid beta (Aβ) plays a crucial role in the nervous system. The misfolding and aggregation of Aβ are primary factors in the progression of Alzheimer's disease (AD). Inhibiting the oligomerization and aggregation of Aβ is considered as an effective strategy against NDs. While it is known that berberine analogs exhibit anti-Aβ aggregation properties, the precise mechanism of action remains unclear. In this study, we have employed computational approaches to unravel the possible mechanism by which berberine combats Aβ aggregation. The introduction of berberine was observed to delay the equilibrium of Aβ16-21 oligomerization. Initially, within the first 10 ns of simulation, β-sheets content was 12.89 % and gradually increased to 22.19 % within the first 20 ns. This upward trend continued, reaching 32.80 %. However, berberine substantially reduced the formation of β-sheets to 1.36 %. These findings decipher the potency of berberine against Aβ16-21 oligomerization, a crucial step for β-sheet formation. Additionally, a remarkable decrease in total number of hydrogen bonds was found in the presence of berberine. Berberine also led to a slight reduction in the flexibility of Aβ16-21, which may be due to the formation of a more stable structures. This study offers valuable insights at the mechanistic level, which could prove beneficial in the development of new drugs to combat NDs.
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Affiliation(s)
- Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Nagma Parveen
- Department of Zoology, Saifia College, Barkatullah University, Bhopal, Madhya Pradesh, India
| | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Furkan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, UP, India.
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21
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Hachlica N, Kolodziejczyk A, Rawski M, Górecki M, Wajda A, Kaczor A. "Nature or nurture" - How environmental factors influence the conformational memory of amyloid fibrils. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123293. [PMID: 37683433 DOI: 10.1016/j.saa.2023.123293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]
Abstract
Amyloid fibrils are complex protein structures with multilayered chiral architecture, that are known to self-propagate. The replication of the mother seed structure by daughter fibrils is known as conformational or templated memory. Using vibrational circular dichroism (VCD), electronic circular dichroism (ECD), transmission electron microscopy (TEM), and cryo-electron microscopy (cryo-EM) we have shown that environmental factors (here agitation) can be a competing force against the templated growth of human lysozyme fibrils. In the cross-seeding experiment non-agitated daughters preserved the structure of agitated mothers, whereas agitated daughters did not always exhibit the same characteristics as their non-agitated mothers. This pattern was reflected on various levels of fibril architecture (secondary structure, protofilament handedness, morphology), demonstrating that the structural indeterminism originates from deeper levels of the fibril structure. This observation may contribute to a better understanding of the processes behind fibril formation.
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Affiliation(s)
- Natalia Hachlica
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Aleksandra Kolodziejczyk
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Michal Rawski
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Aleksandra Wajda
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland.
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22
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Mazzetti S, Giampietro F, Calogero AM, Isilgan HB, Gagliardi G, Rolando C, Cantele F, Ascagni M, Bramerio M, Giaccone G, Isaias IU, Pezzoli G, Cappelletti G. Linking acetylated α-Tubulin redistribution to α-Synuclein pathology in brain of Parkinson's disease patients. NPJ Parkinsons Dis 2024; 10:2. [PMID: 38167511 PMCID: PMC10761989 DOI: 10.1038/s41531-023-00607-9] [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: 02/07/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Highly specialized microtubules in neurons are crucial to both health and disease of the nervous system, and their properties are strictly regulated by different post-translational modifications, including α-Tubulin acetylation. An imbalance in the levels of acetylated α-Tubulin has been reported in experimental models of Parkinson's disease (PD) whereas pharmacological or genetic modulation that leads to increased acetylated α-Tubulin successfully rescues axonal transport defects and inhibits α-Synuclein aggregation. However, the role of acetylation of α-Tubulin in the human nervous system is largely unknown as most studies are based on in vitro evidence. To capture the complexity of the pathological processes in vivo, we analysed post-mortem human brain of PD patients and control subjects. In the brain of PD patients at Braak stage 6, we found a redistribution of acetylated α-Tubulin, which accumulates in the neuronal cell bodies in subcortical structures but not in the cerebral cortex, and decreases in the axonal compartment, both in putamen bundles of fibres and in sudomotor fibres. High-resolution and 3D reconstruction analysis linked acetylated α-Tubulin redistribution to α-Synuclein oligomerization and to phosphorylated Ser 129 α-Synuclein, leading us to propose a model for Lewy body (LB) formation. Finally, in post-mortem human brain, we observed threadlike structures, resembling tunnelling nanotubes that contain α-Synuclein oligomers and are associated with acetylated α-Tubulin enriched neurons. In conclusion, we support the role of acetylated α-Tubulin in PD pathogenesis and LB formation.
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Affiliation(s)
- Samanta Mazzetti
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.
- Fondazione Grigioni per il Morbo di Parkinson, Milan, Italy.
| | | | - Alessandra Maria Calogero
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
- Fondazione Grigioni per il Morbo di Parkinson, Milan, Italy
| | | | - Gloria Gagliardi
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Chiara Rolando
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Francesca Cantele
- Department of Chemistry, Università degli Studi di Milano, Milan, Italy
| | - Miriam Ascagni
- Unitech NOLIMITS, Università degli Studi di Milano, Milan, Italy
| | - Manuela Bramerio
- S. C. Divisione Oncologia Falck and S. C. Divisione Anatomia Patologica, Ospedale Niguarda Ca' Granda, Milan, Italy
| | - Giorgio Giaccone
- Unit of Neuropathology and Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Ioannis Ugo Isaias
- Parkinson Institute, ASST G. Pini-CTO, Milan, Milan, Italy
- Department of Neurology, University Hospital of Würzburg and the Julius Maximilian University of Würzburg, 97080, Würzburg, Germany
| | - Gianni Pezzoli
- Fondazione Grigioni per il Morbo di Parkinson, Milan, Italy
| | - Graziella Cappelletti
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.
- Center of Excellence on Neurodegenerative Diseases, Università degli Studi di Milano, Milan, Italy.
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23
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Lucignano R, Spadaccini R, Merlino A, Ami D, Natalello A, Ferraro G, Picone D. Structural insights and aggregation propensity of a super-stable monellin mutant: A new potential building block for protein-based nanostructured materials. Int J Biol Macromol 2024; 254:127775. [PMID: 38287601 DOI: 10.1016/j.ijbiomac.2023.127775] [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: 08/28/2023] [Revised: 10/12/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Protein fibrillation is commonly associated with pathologic amyloidosis. However, under appropriate conditions several proteins form fibrillar structures in vitro that can be used for biotechnological applications. MNEI and its variants, firstly designed as single chain derivatives of the sweet protein monellin, are also useful models for protein fibrillary aggregation studies. In this work, we have drawn attention to a protein dubbed Mut9, already characterized as a "super stable" MNEI variant. Comparative analysis of the respective X-ray structures revealed how the substitutions present in Mut9 eliminate several unfavorable interactions and stabilize the global structure. Molecular dynamic predictions confirmed the presence of a hydrogen-bonds network in Mut9 which increases its stability, especially at neutral pH. Thioflavin-T (ThT) binding assays and Fourier transform infrared (FTIR) spectroscopy indicated that the aggregation process occurs both at acidic and neutral pH, with and without addition of NaCl, even if with a different kinetics. Accordingly, Transmission Electron Microscopy (TEM) showed a fibrillar organization of the aggregates in all the tested conditions, albeit with some differences in the quantity and in the morphology of the fibrils. Our data underline the great potential of Mut9, which combines great stability in solution with the versatile conversion into nanostructured biomaterials.
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Affiliation(s)
- Rosanna Lucignano
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy
| | - Roberta Spadaccini
- Department of Science and Technology, University of Sannio, Via de Sanctis, 82100 Benevento, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 20126 Milano, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 20126 Milano, Italy
| | - Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy.
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126 Naples, Italy.
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24
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Carroll JA, Striebel JF, Baune C, Chesebro B, Race B. CD11c is not required by microglia to convey neuroprotection after prion infection. PLoS One 2023; 18:e0293301. [PMID: 37910561 PMCID: PMC10619787 DOI: 10.1371/journal.pone.0293301] [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: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Prion diseases are caused by the misfolding of a normal host protein that leads to gliosis, neuroinflammation, neurodegeneration, and death. Microglia have been shown to be critical for neuroprotection during prion infection of the central nervous system (CNS), and their presence extends survival in mice. How microglia impart these benefits to the infected host are unknown. Previous transcriptomics and bioinformatics studies suggested that signaling through the heterodimeric integrin receptor CD11c/CD18, expressed by microglia in the brain, might be important to microglial function during prion disease. Herein, we intracerebrally challenged CD11c-/- mice with prion strain RML and compared them to similarly infected C57BL/6 mice as controls. We initially assessed changes in the brain that are associated with disease such as astrogliosis, microgliosis, prion accumulation, and survival. Targeted qRT-PCR arrays were used to determine alterations in transcription in mice in response to prion infection. We demonstrate that expression of Itgax (CD11c) and Itgb2 (CD18) increases in the CNS in correlation with advancing prion infection. Gliosis, neuropathology, prion deposition, and disease progression in prion infected CD11c deficient mice were comparable to infected C57BL/6 mice. Additionally, both CD11c deficient and C57BL/6 prion-infected mouse cohorts had a similar consortium of inflammatory- and phagocytosis-associated genes that increased as disease progressed to clinical stages. Ingenuity Pathway Analysis of upregulated genes in infected C57BL/6 mice suggested numerous cell-surface transmembrane receptors signal through Spleen Tyrosine Kinase, a potential key regulator of phagocytosis and innate immune activation in the prion infected brain. Ultimately, the deletion of CD11c did not influence prion pathogenesis in mice and CD11c signaling is not involved in the neuroprotection provided by microglia, but our analysis identified a conspicuous phagocytosis pathway in the CNS of infected mice that appeared to be activated during prion pathogenesis.
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Affiliation(s)
- James A. Carroll
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - James F. Striebel
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Chase Baune
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Bruce Chesebro
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brent Race
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
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25
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Soto P, Bravo-Risi F, Benavente R, Lichtenberg S, Lockwood M, Reed JH, Morales R. Identification of chronic wasting disease prions in decaying tongue tissues from exhumed white-tailed deer. mSphere 2023; 8:e0027223. [PMID: 37800903 PMCID: PMC10597447 DOI: 10.1128/msphere.00272-23] [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: 05/16/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023] Open
Abstract
Chronic wasting disease (CWD) prions cause fatal neuropathies in farmed and free-ranging cervids. The deposition of prions in natural and humanmade environmental components has been implicated as a major mechanism mediating CWD spread in wild and captive populations. Prions can be deposited in the environment through excreta, tissues, and carcasses from pre-clinical and clinical animals. Furthermore, burial of CWD-positive animals may reduce but not completely mitigate prion spread from carcasses into the surrounding environment. Here, we analyzed exhumed, decaying deer carcasses for the presence of CWD prions. By analyzing tongue tissues through the protein misfolding cyclic amplification (PMCA) technique, we were able to identify seven out of 95 exhumed white-tailed deer carcasses as CWD prions carriers. Confirmatory analyses were performed using the real-time quaking-induced conversion (RT-QuIC) technique. In addition, we evaluated the potential contamination of the pens that housed these animals by swabbing feeders and waterers. PMCA analyses of swabs confirmed CWD contamination on farming equipment. This work demonstrates the usefulness of PMCA to detect CWD prions in a variety of contexts, including exhumed/decaying tissues. In addition, this is the first report demonstrating swabbing coupled with PMCA as a method for the detection of prion seeding activity on naturally exposed surfaces. Considering that this study was focused on a single site, further studies should confirm whether prion amplification assays are useful to identify CWD prions not only in animals but also in the environment that contains them. IMPORTANCE Environmental contamination is thought to be a major player in the spread of chronic wasting disease (CWD), a fatal prion disease affecting a wide variety of cervid species. At present, there are no officially approved methods allowing for the detection of prion infectivity in environmental components. Importantly, animal as well as anthropogenic activities are thought to contribute to prion environmental contamination. Here, we detected CWD prions in exhumed white-tailed deer carcasses by using the protein misfolding cyclic amplification (PMCA) assay. In addition, we identified CWD prions in feeders used within the infected facility. These results highlight the potential role of PMCA in identifying prion infectivity in a variety of scenarios, ranging from decaying tissues to farming equipment.
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Affiliation(s)
- Paulina Soto
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Francisca Bravo-Risi
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Rebeca Benavente
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Stuart Lichtenberg
- Department of Veterinary and Biomedical Sciences, Minnesota Prion Research and Outreach Center, University of Minnesota, Saint Paul, Minnesota, USA
| | - Mitch Lockwood
- Texas Parks and Wildlife Department, Kerrville, Texas, USA
| | - J. Hunter Reed
- Texas Parks and Wildlife Department, Kerrville, Texas, USA
| | - Rodrigo Morales
- Department of Neurology, The University of Texas Health Science Center at Houston, Houston, Texas, USA
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
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26
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Taha HB, Chawla E, Bitan G. IM-MS and ECD-MS/MS Provide Insight into Modulation of Amyloid Proteins Self-Assembly by Peptides and Small Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2066-2086. [PMID: 37607351 DOI: 10.1021/jasms.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Neurodegenerative proteinopathies are characterized by formation and deposition of misfolded, aggregated proteins in the nervous system leading to neuronal dysfunction and death. It is widely believed that metastable oligomers of the offending proteins, preceding the fibrillar aggregates found in the tissue, are the proximal neurotoxins. There are currently almost no disease-modifying therapies for these diseases despite an active pipeline of preclinical development and clinical trials for over two decades, largely because studying the metastable oligomers and their interaction with potential therapeutics is notoriously difficult. Mass spectrometry (MS) is a powerful analytical tool for structural investigation of proteins, including protein-protein and protein-ligand interactions. Specific MS tools have been useful in determining the composition and conformation of abnormal protein oligomers involved in proteinopathies and the way they interact with drug candidates. Here, we analyze critically the utilization of ion-mobility spectroscopy-MS (IM-MS) and electron-capture dissociation (ECD) MS/MS for analyzing the oligomerization and conformation of multiple amyloidogenic proteins. We also discuss IM-MS investigation of their interaction with two classes of compounds developed by our group over the last two decades: C-terminal fragments derived from the 42-residue form of amyloid β-protein (Aβ42) and molecular tweezers. Finally, we review the utilization of ECD-MS/MS for elucidating the binding sites of the ligands on multiple proteins. These approaches are readily applicable to future studies addressing similar questions and hold promise for facilitating the development of successful disease-modifying drugs against neurodegenerative proteinopathies.
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Affiliation(s)
- Hash Brown Taha
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Integrative Biology & Physiology, University of California Los Angeles, California 90095, United States
| | - Esha Chawla
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Neurology, University of California Los Angeles, California 90095, United States
- Brain Research Institute, University of California Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California Los Angeles, California 90095, United States
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27
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Feng J, She Y, Li C, Shen L. Metal ion mediated aggregation of Alzheimer's disease peptides and proteins in solutions and at surfaces. Adv Colloid Interface Sci 2023; 320:103009. [PMID: 37776735 DOI: 10.1016/j.cis.2023.103009] [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: 06/20/2023] [Revised: 08/29/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Although the pathogenesis of Alzheimer's disease (AD) is still unclear, abnormally high concentrations of metal ions, like copper, iron and zinc, were found in senile plaques of AD brain, which inspires extensive studies on the fundamental molecular interactions of metal ions with the pathogenic hallmarks, amyloid-β (Aβ) peptides and tau proteins, respectively forming senile plaques and neurofibrillary tangles (NFTs) in AD brains. Early works concern the concentration effect of the metal ions on Aβ and tau aggregation. Yet, it is obvious that the surrounding environment of the metal ions must also be considered, not just the metal ions as free accessible forms in the solution phase. The most important surrounding environment in vivo is a very large surface area from cell membranes and other macromolecular surfaces. These bio-interfaces make the kinetic pathways of metal ion mediated Aβ and tau aggregation radically different from those in the solution phase. To better understand the role of metal ions in AD peptide and protein aggregation, we summarize and discuss the recent achievements in the research of metal ion mediated Aβ and tau aggregation, particularly the corresponding mechanism differences between the solution phase and the surface environment. The metal ion chelation therapy for AD is also discussed from the point of the surface pool of metal ions.
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Affiliation(s)
- Jiahao Feng
- Key Laboratory for Neurodegenerative Diseases Nanomedicine of Hubei Province, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| | - Yifei She
- Key Laboratory for Neurodegenerative Diseases Nanomedicine of Hubei Province, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| | - Chongjia Li
- Key Laboratory for Neurodegenerative Diseases Nanomedicine of Hubei Province, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| | - Lei Shen
- Key Laboratory for Neurodegenerative Diseases Nanomedicine of Hubei Province, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China.
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28
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Ito N, Tsuji M, Adachi N, Nakamura S, Sarkar AK, Ikenaka K, Aguirre C, Kimura AM, Kiuchi Y, Mochizuki H, Teplow DB, Ono K. Extracellular high molecular weight α-synuclein oligomers induce cell death by disrupting the plasma membrane. NPJ Parkinsons Dis 2023; 9:139. [PMID: 37770475 PMCID: PMC10539356 DOI: 10.1038/s41531-023-00583-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
α-Synuclein (αS), the causative protein of Parkinson's disease and other α-synucleinopathies, aggregates from a low molecular weight form (LMW-αS) to a high molecular weight αS oligomer (HMW-αSo). Aggregated αS accumulates intracellularly, induces intrinsic apoptosis, is released extracellularly, and appears to propagate disease through prion-like spreading. Whether extracellular αS aggregates are cytotoxic, damage cell wall, or induce cell death is unclear. We investigated cytotoxicity and cell death caused by HMW-αSo or LMW-αS. Extracellular HMW-αSo was more cytotoxic than LMW-αS and was a crucial factor for inducing plasma membrane damage and cell death. HMW-αSo induced reactive oxygen species production and phospholipid peroxidation in the membrane, thereby impairing calcium homeostasis and disrupting plasma membrane integrity. HMW-αSo also induced extrinsic apoptosis and cell death by activating acidic sphingomyelinase. Thus, as extracellular HMW-αSo causes neuronal injury and death via cellular transmission and direct plasma membrane damage, we propose an additional disease progression pathway for α-synucleinopathies.
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Affiliation(s)
- Naohito Ito
- Department of Pharmacology, School of Medicine, Showa University, Tokyo, 142-8555, Japan
- Department of Internal Medicine, Division of Neurology, School of Medicine, Showa University, Tokyo, 142-8666, Japan
| | - Mayumi Tsuji
- Pharmacological Research Center, Showa University, Tokyo, 142-8555, Japan.
| | - Naoki Adachi
- Department of Physiology, School of Medicine, Showa University, Tokyo, 142-8555, Japan
| | - Shiro Nakamura
- Department of Oral Physiology, School of Dentistry, Showa University, Tokyo, 142-8555, Japan
| | - Avijite Kumer Sarkar
- Department of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229-3026, USA
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - César Aguirre
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Atsushi Michael Kimura
- Brain Research Institute Center for Integrated Human Brain Science, Department of Functional Neurology and Neurosurgery, Niigata University, Niigata, 951-8122, Japan
| | - Yuji Kiuchi
- Department of Pharmacology, School of Medicine, Showa University, Tokyo, 142-8555, Japan
- Pharmacological Research Center, Showa University, Tokyo, 142-8555, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - David B Teplow
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles (UCLA), Los Angeles, LA, 10833, USA
| | - Kenjiro Ono
- Department of Neurology, Kanazawa University Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-8640, Japan.
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29
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Zhang Z, Shi M, Li Z, Ling Y, Zhai L, Yuan Y, Ma H, Hao L, Li Z, Zhang Z, Hölscher C. A Dual GLP-1/GIP Receptor Agonist Is More Effective than Liraglutide in the A53T Mouse Model of Parkinson's Disease. PARKINSON'S DISEASE 2023; 2023:7427136. [PMID: 37791037 PMCID: PMC10545468 DOI: 10.1155/2023/7427136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/07/2023] [Accepted: 09/02/2023] [Indexed: 10/05/2023]
Abstract
Parkinson's disease (PD) is a complex syndrome with many elements, such as chronic inflammation, oxidative stress, mitochondrial dysfunction, loss of dopaminergic neurons, build-up of alpha-synuclein (α-syn) in cells, and energy depletion in neurons, that drive the disease. We and others have shown that treatment with mimetics of the growth factor glucagon-like peptide 1 (GLP-1) can normalize energy utilization, neuronal survival, and dopamine levels and reduce inflammation. Liraglutide is a GLP-1 analogue that recently showed protective effects in phase 2 clinical trials in PD patients and in Alzheimer disease patients. We have developed a novel dual GLP-1/GIP receptor agonist that can cross the blood-brain barrier and showed good protective effects in animal models of PD. Here, we test liraglutide against the dual GLP-1/GIP agonist DA5-CH (KP405) in the A53T tg mouse model of PD which expresses a human-mutated gene of α-synuclein. Drug treatment reduced impairments in three different motor tests, reduced levels of α-syn in the substantia nigra, reduced the inflammation response and proinflammatory cytokine levels in the substantia nigra and striatum, and normalized biomarker levels of autophagy and mitochondrial activities in A53T mice. DA5-CH was superior in almost all parameters measured and therefore may be a better drug treatment for PD than liraglutide.
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Affiliation(s)
- Zijuan Zhang
- School of Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Ming Shi
- School of Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Zhengmin Li
- School of Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Yuan Ling
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Luke Zhai
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Ye Yuan
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - He Ma
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Li Hao
- School of Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Zhonghua Li
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Zhenqiang Zhang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
| | - Christian Hölscher
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, Henan, China
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30
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Suthar SK, Lee SY. Truncation or proteolysis of α-synuclein in Parkinsonism. Ageing Res Rev 2023; 90:101978. [PMID: 37286088 DOI: 10.1016/j.arr.2023.101978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 05/28/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023]
Abstract
Posttranslational modifications of α-synuclein, such as truncation or abnormal proteolysis, are implicated in Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). A key focus of this article includes the proteases responsible for inducing truncation, the specific sites susceptible to truncation, and the resultant influence of these truncated species on the seeding and aggregation of endogenous α-synuclein. We also shed light on the unique structural attributes of these truncated species, and how these modifications can lead to distinctive forms of synucleinopathies. In addition, we explore the comparative toxic potentials of various α-synuclein species. An extensive analysis of available evidence of truncated α-synuclein species in human-synucleinopathy brains is also provided. Lastly, we delve into the detrimental impact of truncated species on key cellular structures such as the mitochondria and endoplasmic reticulum. Our article discusses enzymes involved in α-synuclein truncation, including 20 S proteasome, cathepsins, asparagine endopeptidase, caspase-1, calpain-1, neurosin/kallikrein-6, matrix metalloproteinase-1/-3, and plasmin. Truncation patterns impact α-synuclein aggregation - C-terminal truncation accelerates aggregation with larger truncations correlated with shortened aggregation lag times. N-terminal truncation affects aggregation differently based on the truncation location. C-terminally truncated α-synuclein forms compact, shorter fibrils compared to the full-length (FL) protein. N-terminally truncated monomers form fibrils similar in length to FL α-synuclein. Truncated forms show distinct fibril morphologies, increased β-sheet structures, and greater protease resistance. Misfolded α-synuclein can adopt various conformations, leading to unique aggregates and distinct synucleinopathies. Fibrils, with prion-like transmission, are potentially more toxic than oligomers, though this is still debated. Different α-synuclein variants with N- and C-terminal truncations, namely 5-140, 39-140, 65-140, 66-140, 68-140, 71-140, 1-139, 1-135, 1-133, 1-122, 1-119, 1-115, 1-110, and 1-103 have been found in PD, DLB, and MSA patients' brains. In Parkinsonism, excess misfolded α-synuclein overwhelms the proteasome degradation system, resulting in truncated protein production and accumulation in the mitochondria and endoplasmic reticulum.
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Affiliation(s)
| | - Sang-Yoon Lee
- Neuroscience Research Institute, Gachon University, Incheon, South Korea; Department of Neuroscience, College of Medicine, Gachon University, Incheon, South Korea.
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31
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Chatterjee T, Das G, Chatterjee BK, Ghosh S, Chakrabarti P. The Role of Protein- L-isoaspartyl Methyltransferase (PIMT) in the Suppression of Toxicity of the Oligomeric Form of Aβ42, in Addition to the Inhibition of Its Fibrillization. ACS Chem Neurosci 2023; 14:2888-2901. [PMID: 37535852 DOI: 10.1021/acschemneuro.3c00281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
The oligomeric form of amyloid-β peptide (Aβ42) plays a crucial role in the pathogenesis of Alzheimer's disease (AD) and is responsible for cognitive deficits. The soluble oligomers are believed to be more toxic compared to the fibril form. Protein-L-isoaspartyl methyltransferase (PIMT) is a repair enzyme that converts aberrant isoAsp residues, formed spontaneously on isomerization of normal Asp and Asn residues, back to typical Asp. It was shown to inhibit the fibrillization of Aβ42 (containing three Asp residues), and here, we investigate its effect on the size, conformation, and toxicity of Aβ42 oligomers (AβO). Far-UV CD indicated a shift in the conformational feature of AβOs from the random coil to β-sheet in the presence of PIMT. Binding of bis-ANS to different AβOs (obtained using different concentrations of Aβ42 monomer) indicated the correlation of size of oligomers to hydrophobicity: the smallest AβO having the highest hydrophobicity is the most toxic. Dynamic light scattering showed an increase in size of AβO with the addition of PIMT, a contrasting role to that on Aβ fibril. Assays using PC12-derived neurons showed the neuroprotective role of PIMT against AβO-induced toxicity. Furthermore, we have elaborated on the molecular mechanism of the antifibrillar action of PIMT and how this function is correlated with its enzymatic activity. PIMT has a more pronounced effect on AβO as compared to a small heat shock protein, pointing to its importance for the amelioration of the adverse effect of both Aβ42 oligomers and fibrils.
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Affiliation(s)
- Tanaya Chatterjee
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Gaurav Das
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Barun K Chatterjee
- Department of Physics, Bose Institute, 93/1 A.P.C. Road, Kolkata 700054, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
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32
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Price DL, Khan A, Angers R, Cardenas A, Prato MK, Bani M, Bonhaus DW, Citron M, Biere AL. In vivo effects of the alpha-synuclein misfolding inhibitor minzasolmin supports clinical development in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:114. [PMID: 37460603 PMCID: PMC10352257 DOI: 10.1038/s41531-023-00552-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
Direct targeting of alpha-synuclein (ASYN) has emerged as a disease-modifying strategy for Parkinson's disease and other synucleinopathies which is being approached using both small molecule compounds and ASYN-targeted biologics. Minzasolmin (UCB0599) is an orally bioavailable and brain-penetrant small molecule ASYN misfolding inhibitor in clinical development as a disease-modifying therapeutic for Parkinson's disease. Herein the results of preclinical evaluations of minzasolmin that formed the basis for subsequent clinical development are described. Pharmacokinetic evaluations of intraperitoneal 1 and 5 mg/kg minzasolmin in wildtype mice revealed parallel and dose-proportional exposures in brain and plasma. Three-month administration studies in the Line 61 transgenic mouse model of PD were conducted to measure ASYN pathology and other PD-relevant endpoints including markers of CNS inflammation, striatal DAT labeling and gait. Reductions in ASYN pathology were correlated with improved aspects of gait and balance, reductions in CNS inflammation marker abundance, and normalized striatal DAT levels. These findings provide support for human dose determinations and have informed the translational strategy for clinical trial design and biomarker selection for the ongoing clinical studies of minzasolmin in patients living with early-stage Parkinson's disease (ClinicalTrials.gov ID: NCT04658186; EudraCT Number 2020-003265).
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Affiliation(s)
| | - Asma Khan
- Neuropore Therapies, Inc., San Diego, CA, USA
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Jain MK, Bhat R. Modulation of the conformation, fibrillation, and fibril morphologies of human brain α-, β-, and γ-syn proteins by the disaccharide chemical chaperone trehalose. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023:140932. [PMID: 37433401 DOI: 10.1016/j.bbapap.2023.140932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/13/2023]
Abstract
Human α-, β-, and γ-synuclein (syn) are natively unfolded proteins present in the brain. Deposition of aggregated α-syn in Lewy bodies is associated with Parkinson's disease (PD) and γ-syn is known to be involved in both neurodegeneration and breast cancer. At physiological pH, while α-syn has the highest propensity for fibrillation followed by γ-syn, β-syn does not form any fibrils. Fibril formation in these proteins could be modulated by protein structure stabilizing osmolytes such as trehalose which has an exceptional stabilizing effect for globular proteins. We present a comprehensive study of the effect of trehalose on the conformation, aggregation, and fibril morphology of α-, β-, and γ-syn proteins. Rather than stabilizing the intrinsically disordered state of the synucleins, trehalose accelerates the rate of fibril formation by forming aggregation-competent partially folded intermediate structures. Fibril morphologies are also strongly dependent on the concentration of trehalose with ≤ 0.4M favoring the formation of mature fibrils in α-, and γ-syn with no effect on the fibrillation of β-syn. At ≥ 0.8M, trehalose promotes the formation of smaller aggregates that are more cytotoxic. Live cell imaging of preformed aggregates of a labeled A90C α-syn shows their rapid internalization into neural cells which could be useful in reducing the load of aggregated species of α-syn. The findings throw light on the differential effect of trehalose on the conformation and aggregation of disordered synuclein proteins with respect to globular proteins and could help in understanding the effect of osmolytes on intrinsically disordered proteins under cellular stress conditions.
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Affiliation(s)
- Manish K Jain
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India; Department of Pharmacology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India.
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Noguchi-Shinohara M, Ono K. The Mechanisms of the Roles of α-Synuclein, Amyloid-β, and Tau Protein in the Lewy Body Diseases: Pathogenesis, Early Detection, and Therapeutics. Int J Mol Sci 2023; 24:10215. [PMID: 37373401 DOI: 10.3390/ijms241210215] [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: 05/22/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Lewy body diseases (LBD) are pathologically defined as the accumulation of Lewy bodies composed of an aggregation of α-synuclein (αSyn). In LBD, not only the sole aggregation of αSyn but also the co-aggregation of amyloidogenic proteins, such as amyloid-β (Aβ) and tau, has been reported. In this review, the pathophysiology of co-aggregation of αSyn, Aβ, and tau protein and the advancement in imaging and fluid biomarkers that can detect αSyn and co-occurring Aβ and/or tau pathologies are discussed. Additionally, the αSyn-targeted disease-modifying therapies in clinical trials are summarized.
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Affiliation(s)
- Moeko Noguchi-Shinohara
- Department of Neurology, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
| | - Kenjiro Ono
- Department of Neurology, Kanazawa University Graduate School of Medical Sciences, Kanazawa 920-8640, Japan
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35
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Chen X, Xing L, Li X, Chen N, Liu L, Wang J, Zhou X, Liu S. Manganese Ion-Induced Amyloid Fibrillation Kinetics of Hen Egg White-Lysozyme in Thermal and Acidic Conditions. ACS OMEGA 2023; 8:16439-16449. [PMID: 37179629 PMCID: PMC10173442 DOI: 10.1021/acsomega.3c01531] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
As manganese ions (Mn2+) are identified as an environmental risk factor for neurodegenerative diseases, uncovering their action mechanism on protein amyloid fibril formation is crucial for related disease treatments. Herein, we performed a combined study of Raman spectroscopy, atomic force microscopy (AFM), thioflavin T (ThT) fluorescence, and UV-vis absorption spectroscopy assays, in which the distinctive effect of Mn2+ on the amyloid fibrillation kinetics of hen egg white-lysozyme (HEWL) was clarified at the molecular level. With thermal and acid treatments, the unfolding of protein tertiary structures is efficiently accelerated by Mn2+ to form oligomers, as indicated by two Raman markers for the Trp residues on protein side chains: the FWHM at 759 cm-1 and the I1340/I1360 ratio. Meanwhile, the inconsistent evolutionary kinetics of the two indicators, as well as AFM images and UV-vis absorption spectroscopy assays, validate the tendency of Mn2+ toward the formation of amorphous aggregates instead of amyloid fibrils. Moreover, Mn2+ plays an accelerator role in the secondary structure transition from α-helix to organized β-sheet structures, as indicated by the N-Cα-C intensity at 933 cm-1 and the amide I position of Raman spectroscopy and ThT fluorescence assays. Notably, the more significant promotion effect of Mn2+ on the formation of amorphous aggregates provides credible clues to understand the fact that excess exposure to manganese is associated with neurological diseases.
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Affiliation(s)
- Xiaodong Chen
- Department
of Chemical Physics, University of Science
and Technology of China, Hefei 230026, China
| | - Lei Xing
- State
Key Laboratory of Analytical Chemistry for Life Science, School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, China
| | - Xinfei Li
- Department
of Chemical Physics, University of Science
and Technology of China, Hefei 230026, China
| | - Ning Chen
- Department
of Chemical Physics, University of Science
and Technology of China, Hefei 230026, China
| | - Liming Liu
- Department
of Chemical Physics, University of Science
and Technology of China, Hefei 230026, China
| | - Jionghan Wang
- Department
of Chemical Physics, University of Science
and Technology of China, Hefei 230026, China
| | - Xiaoguo Zhou
- Department
of Chemical Physics, University of Science
and Technology of China, Hefei 230026, China
| | - Shilin Liu
- Department
of Chemical Physics, University of Science
and Technology of China, Hefei 230026, China
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Martins GF, Nascimento C, Galamba N. Mechanistic Insights into Polyphenols' Aggregation Inhibition of α-Synuclein and Related Peptides. ACS Chem Neurosci 2023; 14:1905-1920. [PMID: 37125909 DOI: 10.1021/acschemneuro.3c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
While several polyphenols were found to either inhibit or modulate the aggregation of proteins implicated in neurodegenerative diseases, such as Parkinson's disease (PD), discrepant action mechanisms have been reported. This, in addition to some polyphenols' pan-assay interference compounds' reputation, casts some doubts concerning their therapeutic relevance. Here, we studied, through molecular dynamics and enhanced sampling methods, the aggregation of 11-mer peptides from the non-amyloid-β component, an aggregation-prone domain of α-synuclein (α-syn) implicated in PD and other synucleinopathies, in neat water and aqueous solutions of resveratrol (RSV) and gallic acid (GA). Further, simulations of the complete protein were carried out in aqueous urea, RSV, and GA solutions. Our results show that peptide aggregation is not disrupted by either phenolic compound. Thus, instead, intrusion of RSV and GA in the inter-peptide region induces a peptide-peptide re-orientation, favoring terminal interactions that manifest in the formation of barrierless solvent-separated configurations. Moreover, although the (poly)phenols induce a pronounced peptide dewetting at high concentrations, β-sheet-rich regions, a hallmark of α-syn aggregation, are not disrupted. Thus, our results indicate that, if anything, RSV and GA delay or modulate peptide aggregation at high concentrations via the stabilization of solvent-separated conformations as opposed to aggregation inhibition. Structural analysis of the full protein, however, shows that the (poly)phenols induce more extended conformations of α-syn, similar to urea, possibly also influencing its aggregation propensity. However, opposite to urea, the (poly)phenols reduce α-syn's conformational space, likely due to steric effects and a slowdown of the solvent dynamics. These effects are concentration-dependent and possibly unattainable at therapeutic-relevant concentrations. These results suggest that the aggregation inhibition activity of RSV and GA in vitro should involve, instead, either the non-covalent binding to oligomeric intermediates or the stabilization of the monomer and/or oligomers through the formation of covalent bonds of the respective quinones with α-syn. In addition, the enhanced aggregation tendency of the peptides observed here could be associated with the formation of non-toxic oligomers, reported for some polyphenols.
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Affiliation(s)
- G F Martins
- BioISI─Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, Lisbon 1749-016, Portugal
| | - C Nascimento
- BioISI─Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, Lisbon 1749-016, Portugal
| | - N Galamba
- BioISI─Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, Lisbon 1749-016, Portugal
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Zhou Y, Li Q, Wu Y, Li X, Zhou Y, Wang Z, Liang H, Ding F, Hong S, Steinmetz NF, Cai H. Molecularly Stimuli-Responsive Self-Assembled Peptide Nanoparticles for Targeted Imaging and Therapy. ACS NANO 2023; 17:8004-8025. [PMID: 37079378 DOI: 10.1021/acsnano.3c01452] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly has emerged as an extensively used method for constructing biomaterials with sizes ranging from nanometers to micrometers. Peptides have been extensively investigated for self-assembly. They are widely applied owing to their desirable biocompatibility, biodegradability, and tunable architecture. The development of peptide-based nanoparticles often requires complex synthetic processes involving chemical modification and supramolecular self-assembly. Stimuli-responsive peptide nanoparticles, also termed "smart" nanoparticles, capable of conformational and chemical changes in response to stimuli, have emerged as a class of promising materials. These smart nanoparticles find a diverse range of biomedical applications, including drug delivery, diagnostics, and biosensors. Stimuli-responsive systems include external stimuli (such as light, temperature, ultrasound, and magnetic fields) and internal stimuli (such as pH, redox environment, salt concentration, and biomarkers), facilitating the generation of a library of self-assembled biomaterials for biomedical imaging and therapy. Thus, in this review, we mainly focus on peptide-based nanoparticles built by self-assembly strategy and systematically discuss their mechanisms in response to various stimuli. Furthermore, we summarize the diverse range of biomedical applications of peptide-based nanomaterials, including diagnosis and therapy, to demonstrate their potential for medical translation.
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Affiliation(s)
- Yang Zhou
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Qianqian Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Ye Wu
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Xinyu Li
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Ya Zhou
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Zhu Wang
- Department of Urology, Affiliated People's Hospital of Longhua Shenzhen, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong 518109, PR China
| | - Hui Liang
- Department of Urology, Affiliated People's Hospital of Longhua Shenzhen, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong 518109, PR China
| | - Feiqing Ding
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Sheng Hong
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Nicole F Steinmetz
- Department of NanoEngineering, Department of Biongineering, Department of Radiology, Moores Cancer Center, Center for Nano-ImmunoEngineering, Center for Engineering in Cancer, Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, California 92093, United States
| | - Hui Cai
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-Sen University, 66 Gongchang Road, Guangming District, Shenzhen 518107, China
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Razzokov J, Fazliev S, Makhkamov M, Marimuthu P, Baev A, Kurganov E. Effect of Electric Field on α-Synuclein Fibrils: Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24076312. [PMID: 37047286 PMCID: PMC10094641 DOI: 10.3390/ijms24076312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The self-association of amylogenic proteins to the fibril form is considered a pivotal factor in the pathogenesis of neurodegenerative diseases, including Parkinson’s disease (PD). PD causes unintended or uncontrollable movements in its common symptoms. α-synuclein is the major cause of PD development and thus has been the main target of numerous studies to suppress and sequester its expression or effectively degrade it. Nonetheless, to date, there are no efficient and proven ways to prevent pathological protein aggregation. Recent investigations proposed applying an external electric field to interrupt the fibrils. This method is a non-invasive approach that has a certain benefit over others. We performed molecular dynamics (MD) simulations by applying an electric field on highly toxic fibrils of α-synuclein to gain a molecular-level insight into fibril disruption mechanisms. The results revealed that the applied external electric field induces substantial changes in the conformation of the α-synuclein fibrils. Furthermore, we show the threshold value for electric field strength required to completely disrupt the α-synuclein fibrils by opening the hydrophobic core of the fibril. Thus, our findings might serve as a valuable foundation to better understand molecular-level mechanisms of the α-synuclein fibrils disaggregation process under an applied external electric field.
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Affiliation(s)
- Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- R&D Center, New Uzbekistan University, Mustaqillik Avenue 54, Tashkent 100007, Uzbekistan
- Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, Tashkent 100084, Uzbekistan
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
- Correspondence: ; Tel.: +998-90-116-23-20
| | - Sunnatullo Fazliev
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
- Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Mukhriddin Makhkamov
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
| | - Parthiban Marimuthu
- Pharmaceutical Science Laboratory (PSL–Pharmacy) and Structural Bioinformatics Laboratory (SBL–Biochemistry), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Artyom Baev
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
- Department of Biophysics, Biological Faculty, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
| | - Erkin Kurganov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Hoppenreijs LJ, Brune SE, Biedendieck R, Krull R, Boom RM, Keppler JK. Fibrillation of β-lactoglobulin at pH 2.0: Impact of cysteine substitution and disulfide bond reduction intended for food Hydrocolloids. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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40
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The interactions of amyloid β aggregates with phospholipid membranes and the implications for neurodegeneration. Biochem Soc Trans 2023; 51:147-159. [PMID: 36629697 DOI: 10.1042/bst20220434] [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: 09/14/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023]
Abstract
Misfolding, aggregation and accumulation of Amyloid-β peptides (Aβ) in neuronal tissue and extracellular matrix are hallmark features of Alzheimer's disease (AD) pathology. Soluble Aβ oligomers are involved in neuronal toxicity by interacting with the lipid membrane, compromising its integrity, and affecting the function of receptors. These facts indicate that the interaction between Aβ oligomers and cell membranes may be one of the central molecular level factors responsible for the onset of neurodegeneration. The present review provides a structural understanding of Aβ neurotoxicity via membrane interactions and contributes to understanding early events in Alzheimer's disease.
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Dabiri S, Ramírez Ruiz MI, Jean-Louis G, Ntekim OE, Obisesan TO, Campbell AL, Mwendwa DT. The Mediating Role of Inflammation in the Relationship Between α-Synuclein and Cognitive Functioning. J Gerontol A Biol Sci Med Sci 2023; 78:206-212. [PMID: 36269624 PMCID: PMC10215981 DOI: 10.1093/gerona/glac217] [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: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Accumulating evidence suggests that α-synuclein plays a role in the pathophysiology of Alzheimer's disease (AD). This study examined whether α-synuclein level in cerebrospinal fluid (CSF) was associated with cognitive functioning among older adults. We also explored whether this relationship was mediated by proinflammatory cytokines TNF-α and IL-6, along with sIL-6R and vascular endothelial growth factor (VEGF). Using a cross-sectional Alzheimer's Disease Neuroimaging Initiative (ADNI; N = 148) sample, we examined the relationship between α-synuclein and participants' performance on Mini-Mental State Examination (MMSE) and Alzheimer's Disease Assessment Scale Cognitive Subscale (ADAS-Cog 13) at baseline. Mediation analyses were utilized, adjusting for age, education, APOEe4, and Geriatric Depression Scale scores. All biological markers were measured in CSF. Participants in the current sample were 58.3% males, 41.7% females, and Caucasian (95.5%); their average education and age were 15.5 (standard deviation [SD] = 2.97) and 74.4 (SD = 7.51) years, respectively. Higher accumulation of α-synuclein was associated with poorer MMSE scores (β = -0.41, standard error [SE] = 1.54, p < .001). This relationship appeared to be mediated by VEGF (β = 0.27, SE = 2.15, p = .025) and IL-6r (β = 0.22, SE = 1.66, p < .026). In addition, α-synuclein was associated with poorer performance on the ADAS-Cog 13 (β = 0.34, p = .005) and mediated by VEGF (β = -0.19, SE = 4.13, p = .025) after adjusting for age, education, APOEe4, and depressive symptoms. α-Synuclein may serve as an additional biomarker for determining poor cognitive functioning. VEGF and IL-6 soluble receptors were significant mediators of the relationship between α-synuclein and cognitive functioning. If confirmed in prospective analyses, these findings can further inform the pathologic cascade and early diagnosis of AD.
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Affiliation(s)
- Sanaz Dabiri
- Department of Psychology, Howard University, Washington, District of Columbia, Washington, DC, USA
| | - Mara I Ramírez Ruiz
- Department of Psychology, Howard University, Washington, District of Columbia, Washington, DC, USA
| | - Girardin Jean-Louis
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Oyonumo E Ntekim
- Department of Graduate Nutritional Sciences, Howard University, Washington, District of Columbia, Washington, DC, USA
| | - Thomas O Obisesan
- Division of Geriatrics, Department of Medicine, Howard University Hospital, Washington, District of Columbia, Washington, DC, USA
| | - Alfonso L Campbell
- Department of Psychology, Howard University, Washington, District of Columbia, Washington, DC, USA
| | - Denée T Mwendwa
- Department of Psychology, Howard University, Washington, District of Columbia, Washington, DC, USA
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Matthes D, de Groot BL. Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. J Biol Chem 2023; 299:103034. [PMID: 36806684 PMCID: PMC10033322 DOI: 10.1016/j.jbc.2023.103034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Oligomeric aggregates of the amyloid-beta peptide(1-42) (Aβ42) are regarded as a primary cause of cytotoxicity related to membrane damage in Alzheimer's disease. However, a dynamical and structural characterization of pore-forming Aβ42 oligomers at atomic detail has not been feasible. Here, we used Aβ42 oligomer structures previously determined in a membrane-mimicking environment as putative model systems to study the pore formation process in phospholipid bilayers with all-atom molecular dynamics simulations. Multiple Aβ42 oligomer sizes, conformations, and N-terminally truncated isoforms were investigated on the multi-μs time scale. We found that pore formation and ion permeation occur via edge conductivity and exclusively for β-sandwich structures that feature exposed side-by-side β-strand pairs formed by residues 9 to 21 of Aβ42. The extent of pore formation and ion permeation depends on the insertion depth of hydrophilic residues 13 to 16 (HHQK domain) and thus on subtle differences in the overall stability, orientation, and conformation of the aggregates in the membrane. Additionally, we determined that backbone carbonyl and polar side-chain atoms from the edge strands directly contribute to the coordination sphere of the permeating ions. Furthermore, point mutations that alter the number of favorable side-chain contacts correlate with the ability of the Aβ42 oligomer models to facilitate ion permeation in the bilayer center. Our findings suggest that membrane-inserted, layered β-sheet edges are a key structural motif in pore-forming Aβ42 oligomers independent of their size and play a pivotal role in aggregate-induced membrane permeabilization.
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Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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Tsoi PS, Quan MD, Ferreon JC, Ferreon ACM. Aggregation of Disordered Proteins Associated with Neurodegeneration. Int J Mol Sci 2023; 24:3380. [PMID: 36834792 PMCID: PMC9966039 DOI: 10.3390/ijms24043380] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Cellular deposition of protein aggregates, one of the hallmarks of neurodegeneration, disrupts cellular functions and leads to neuronal death. Mutations, posttranslational modifications, and truncations are common molecular underpinnings in the formation of aberrant protein conformations that seed aggregation. The major proteins involved in neurodegeneration include amyloid beta (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, and TAR DNA-binding protein (TDP-43) in amyotrophic lateral sclerosis (ALS). These proteins are described as intrinsically disordered and possess enhanced ability to partition into biomolecular condensates. In this review, we discuss the role of protein misfolding and aggregation in neurodegenerative diseases, specifically highlighting implications of changes to the primary/secondary (mutations, posttranslational modifications, and truncations) and the quaternary/supramolecular (oligomerization and condensation) structural landscapes for the four aforementioned proteins. Understanding these aggregation mechanisms provides insights into neurodegenerative diseases and their common underlying molecular pathology.
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Affiliation(s)
| | | | - Josephine C. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Allan Chris M. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
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44
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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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45
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Kabir ER, Chowdhury NM, Yasmin H, Kabir MT, Akter R, Perveen A, Ashraf GM, Akter S, Rahman MH, Sweilam SH. Unveiling the Potential of Polyphenols as Anti-Amyloid Molecules in Alzheimer's Disease. Curr Neuropharmacol 2023; 21:787-807. [PMID: 36221865 PMCID: PMC10227919 DOI: 10.2174/1570159x20666221010113812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/03/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disease that mostly affects the elderly population. Mechanisms underlying AD pathogenesis are yet to be fully revealed, but there are several hypotheses regarding AD. Even though free radicals and inflammation are likely to be linked with AD pathogenesis, still amyloid-beta (Aβ) cascade is the dominant hypothesis. According to the Aβ hypothesis, a progressive buildup of extracellular and intracellular Aβ aggregates has a significant contribution to the AD-linked neurodegeneration process. Since Aβ plays an important role in the etiology of AD, therefore Aβ-linked pathways are mainly targeted in order to develop potential AD therapies. Accumulation of Aβ plaques in the brains of AD individuals is an important hallmark of AD. These plaques are mainly composed of Aβ (a peptide of 39-42 amino acids) aggregates produced via the proteolytic cleavage of the amyloid precursor protein. Numerous studies have demonstrated that various polyphenols (PPHs), including cyanidins, anthocyanins, curcumin, catechins and their gallate esters were found to markedly suppress Aβ aggregation and prevent the formation of Aβ oligomers and toxicity, which is further suggesting that these PPHs might be regarded as effective therapeutic agents for the AD treatment. This review summarizes the roles of Aβ in AD pathogenesis, the Aβ aggregation pathway, types of PPHs, and distribution of PPHs in dietary sources. Furthermore, we have predominantly focused on the potential of food-derived PPHs as putative anti-amyloid drugs.
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Affiliation(s)
- Eva Rahman Kabir
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | | | - Hasina Yasmin
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | - Md. Tanvir Kabir
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | - Rokeya Akter
- Department of Pharmacy, Jagannath University, Dhaka, Bangladesh
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Shamima Akter
- Department of Bioinformatics and Computational Biology, George Mason University, Fairfax, Virginia 22030, USA
| | | | - Sherouk Hussein Sweilam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Cairo-Suez Road, Badr City 11829, Egypt
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Abstract
The scientific landscape surrounding amyotrophic lateral sclerosis has shifted immensely with a number of well-defined ALS disease-causing genes, each with related phenotypical and cellular motor neuron processes that have come to light. Yet in spite of decades of research and clinical investigation, there is still no etiology for sporadic amyotrophic lateral sclerosis, and treatment options even for those with well-defined familial syndromes are still limited. This chapter provides a comprehensive review of the genetic basis of amyotrophic lateral sclerosis, highlighting factors that contribute to its heritability and phenotypic manifestations, and an overview of past, present, and upcoming therapeutic strategies.
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Affiliation(s)
- David S Younger
- Department of Clinical Medicine and Neuroscience, CUNY School of Medicine, New York, NY, United States; Department of Medicine, Section of Internal Medicine and Neurology, White Plains Hospital, White Plains, NY, United States.
| | - Robert H Brown
- Department of Neurology, UMass Chan Medical School, Donna M. and Robert J. Manning Chair in Neurosciences and Director in Neurotherapeutics, Worcester, MA, United States
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Pillai M, Jha SK. Multistep molecular mechanism of amyloid-like aggregation of nucleic acid-binding domain of TDP-43. Proteins 2022; 91:649-664. [PMID: 36530161 DOI: 10.1002/prot.26455] [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: 05/02/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
TDP-43 protein is associated with many neurodegenerative diseases and has been shown to adopt various oligomeric and fibrillar states. However, a detailed kinetic understanding of the structural transformation of the native form of the protein to the fibrillar state is missing. In this study, we delineate the temporal sequence of structural events during the amyloid-like assembly of the functional nucleic acid-binding domain of TDP-43. We kinetically mapped the aggregation process using multiple probes such as tryptophan and thioflavin T (ThT) fluorescence, circular dichroism (CD), and dynamic light scattering (DLS) targeting different structural events. Our data reveal that aggregation occurs in four distinct steps-very fast, fast, slow, and very slow. The "very fast" change results in partially unfolded forms that undergo conformational conversion, oligomerization and bind to ThT in the "fast step" to form higher order intermediates (HOI). The temporal sequence of the formation of ThT binding sites and conformational conversion depends upon the protein concentration. The HOI further undergoes structural rearrangement to form protofibrils in the "slow" step, which, consequently, assembles in the "very slow" step to form an amyloid-like assembly. The spectroscopic properties of the amyloid-like assembly across the protein concentration remain similar. Additionally, we observe no lag phase across protein concentration for all the probes studied, suggesting that the aggregation process follows a linear polymerization reaction. Overall, our study demonstrates that the amyloid-like assembly forms in multiple steps, which is also supported by the temperature dependence of the kinetics.
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Affiliation(s)
- Meenakshi Pillai
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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48
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Wu KY, Doan D, Medrano M, Chang CEA. Modeling structural interconversion in Alzheimers' amyloid beta peptide with classical and intrinsically disordered protein force fields. J Biomol Struct Dyn 2022; 40:10005-10022. [PMID: 34152264 DOI: 10.1080/07391102.2021.1939163] [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: 12/16/2022]
Abstract
A comprehensive understanding of the aggregation mechanism in amyloid beta 42 (Aβ42) peptide is imperative for developing therapeutic drugs to prevent or treat Alzheimer's disease. Because of the high flexibility and lack of native tertiary structures of Aβ42, molecular dynamics (MD) simulations may help elucidate the peptide's dynamics with atomic details and collectively improve ensembles not seen in experiments. We applied microsecond-timescale MD simulations to investigate the dynamics and conformational changes of Aβ42 by using a newly developed Amber force field (ff14IDPSFF). We compared the ff14IDPSFF and the regular ff14SB force field by examining the conformational changes of two distinct Aβ42 monomers in explicit solvent. Conformational ensembles obtained by simulations depend on the force field and initial structure, Aβ42α-helix or Aβ42β-strand. The ff14IDPSFF sampled a high ratio of disordered structures and diverse β-strand secondary structures; in contrast, ff14SB favored helicity during the Aβ42α-helix simulations. The conformations obtained from Aβ42β-strand simulations maintained a balanced content in the disordered and helical structures when simulated by ff14SB, but the conformers clearly favored disordered and β-sheet structures simulated by ff14IDPSFF. The results obtained with ff14IDPSFF qualitatively reproduced the NMR chemical shifts well. In-depth peptide and cluster analysis revealed some characteristic features that may be linked to early onset of the fibril-like structure. The C-terminal region (mainly M35-V40) featured in-registered anti-parallel β-strand (β-hairpin) conformations with tested systems. Our work should expand the knowledge of force field and structure dependency in MD simulations and reveals the underlying structural mechanism-function relationship in Aβ42 peptides. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kingsley Y Wu
- Department of Chemistry, University of California, Riverside, CA, USA
| | - David Doan
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Marco Medrano
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA, USA
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49
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Törner R, Kupreichyk T, Hoyer W, Boisbouvier J. The role of heat shock proteins in preventing amyloid toxicity. Front Mol Biosci 2022; 9:1045616. [PMID: 36589244 PMCID: PMC9798239 DOI: 10.3389/fmolb.2022.1045616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The oligomerization of monomeric proteins into large, elongated, β-sheet-rich fibril structures (amyloid), which results in toxicity to impacted cells, is highly correlated to increased age. The concomitant decrease of the quality control system, composed of chaperones, ubiquitin-proteasome system and autophagy-lysosomal pathway, has been shown to play an important role in disease development. In the last years an increasing number of studies has been published which focus on chaperones, modulators of protein conformational states, and their effects on preventing amyloid toxicity. Here, we give a comprehensive overview of the current understanding of chaperones and amyloidogenic proteins and summarize the advances made in elucidating the impact of these two classes of proteins on each other, whilst also highlighting challenges and remaining open questions. The focus of this review is on structural and mechanistic studies and its aim is to bring novices of this field "up to speed" by providing insight into all the relevant processes and presenting seminal structural and functional investigations.
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Affiliation(s)
- Ricarda Törner
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
| | - Tatsiana Kupreichyk
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jerome Boisbouvier
- University Grenoble Alpes, CNRS CEA Institut de Biologie Structurale (IBS), Grenoble, France,*Correspondence: Ricarda Törner, ; Jerome Boisbouvier,
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50
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Wu K, Sun W, Li D, Diao J, Xiu P. Inhibition of Amyloid Nucleation by Steric Hindrance. J Phys Chem B 2022; 126:10045-10054. [PMID: 36417323 DOI: 10.1021/acs.jpcb.2c06330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite recent experiments and simulations suggesting that small-molecule inhibitors and some post-translational modifications (e.g., glycosylation and ubiquitination) can suppress the pathogenic aggregation of proteins due to steric hindrance, the effect of steric hindrance on amyloid formation has not been systematically studied. Based on Monte Carlo simulations using a coarse-grained model for amyloidogenic proteins and a hard sphere acting as steric hindrance, we investigated how steric hindrance on proteins could affect amyloid formation, particularly two steps of primary nucleation, namely, oligomerization and conformational conversion into a β-sheet-enriched nucleus. We found that steric spheres played an inhibitory role in oligomerization with the effect proportional to the sphere radius RS, which we attributed to the decline in the nonspecific attractions between proteins. During the second step, small steric spheres facilitated the conformational conversion of proteins while large ones suppressed the conversion. The overall steric effect on amyloid nucleation was inhibitory regardless of RS. As RS increased, oligomeric assemblies changed from amorphous into sheet-like, structurally ordered species, reminiscent of the structure of amyloid fibrils. The oligomers with large RS were off-pathway with their ordered structures induced by the competition between steric hindrance and nonspecific attractions of soluble proteins. Interestingly, the equimolar mixture of proteins with and without steric hindrance amplified the sterically inhibitory effect by increasing the energy barrier of protein's conformational conversion. The physical mechanisms and biological implications of the above results are discussed. Our findings improve the current understanding of how nature regulates protein aggregation and amyloid formation by steric hindrance.
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Affiliation(s)
- Kai Wu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Wuxuepeng Sun
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Dechang Li
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Peng Xiu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
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