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Hirschbeck SS, Lindberg ET, Jang JH, Jacob MR, Lazar Cantrell KL, Do TD. Investigating a Novel Neurodegenerative Disease Toxic Mechanism Involving Lipid Binding Specificity of Amyloid Oligomers. ACS Chem Neurosci 2024; 15:1523-1532. [PMID: 38488720 DOI: 10.1021/acschemneuro.3c00830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Exploring the mechanisms underlying the toxicity of amyloid oligomers (AOs) presents a significant opportunity for discovering cures and developing treatments for neurodegenerative diseases. Recently, using a combination of ion mobility spectrometry-mass spectrometry (IMS-MS) and X-ray crystallography (XRC), we showed that the peptide KVKVLWDVIEV, which is the G95W mutant of αB-Crystallin (90-100) and abbreviated as G6W, self-assembles up to a dodecamer that structurally resembles lipid transport proteins. The glycine to tryptophan mutation promotes not only larger oligomers and enhanced cytotoxicity in brain slices than the wild type but also a narrow hydrophobic cavity suitable for fatty acid or phospholipid binding. Here, we determine the plausibility of a novel cytotoxic mechanism where the G6W's structural motif could perturb lipid homeostasis by determining its lipid binding selectivity and specificity. We show that the G6W oligomers have a strong affinity toward unsaturated phospholipids with a preference toward phospholipids containing 16-C alkyl chains. Molecular dynamics simulations demonstrate how an unsaturated, 16-C phospholipid fits tightly inside and outside G6W's hydrophobic cavity. This binding is exclusive to the G6W peptide, as other amyloid oligomers with different atomic structures, including its wildtype αB-Crystallin (90-100) and several superoxide dismutase 1 (SOD1) peptides that are known to self-assemble into amyloid oligomers (SOD1P28K and SOD1WG-GW), do not experience the same strong binding affinity. While the existing chaperone-lipid hypothesis on amyloid toxicity suggests amyloid-lipid complexes perforate cell membranes, our work provides a new outlook, indicating that soluble amyloid oligomers disrupt lipid homeostasis via selective protein-ligand interactions. The toxic mechanisms may arise from the formation of unique amyloid oligomer structures assisted by lipid ligands or impaired lipid transports.
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Affiliation(s)
- Sarah S Hirschbeck
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Edward T Lindberg
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Joshua H Jang
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - MaKenna R Jacob
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | | | - Thanh D Do
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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Tooyama I, Kato T, Taguchi H, Kageyama Y, Irie K, Hirahara Y, Yanagisawa D. Visualization of Amyloid Oligomers in the Brain of Patients with Alzheimer's Disease. Acta Histochem Cytochem 2023; 56:87-94. [PMID: 38318103 PMCID: PMC10838628 DOI: 10.1267/ahc.23-00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/22/2023] [Indexed: 02/07/2024] Open
Abstract
In the pathogenesis of Alzheimer's disease (AD), highly neurotoxic amyloid-β (Aβ) oligomers appear early, they are thus considered to be deeply involved in the onset of Alzheimer's disease. However, Aβ oligomer visualization is challenging in human tissues due to their multiple forms (e.g., low- and high-molecular-weight oligomers, including protofibrils) as well as their tendency to rapidly change forms and aggregate. In this review, we present two visualization approaches for Aβ oligomers in tissues: an immunohistochemical (using the monoclonal antibody TxCo1 against toxic Aβ oligomer conformers) and imaging mass spectrometry using the small chemical Shiga-Y51 that specifically binds Aβ oligomers. TxCo1 immunohistochemistry revealed Aβ oligomer distributions in postmortem human brains with AD. Using Shiga-Y51, imaging mass spectrometry revealed Aβ oligomer distributions in the brain of a transgenic mouse model for AD. These two methods would potentially contribute to elucidating the pathological mechanisms underlying AD.
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Affiliation(s)
- Ikuo Tooyama
- Medical Innovation Research Center, Shiga University of Medical Science, Otsu, Japan
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Otsu, Japan
| | - Tomoko Kato
- Medical Innovation Research Center, Shiga University of Medical Science, Otsu, Japan
| | - Hiroyasu Taguchi
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Otsu, Japan
| | - Yusuke Kageyama
- Medical Innovation Research Center, Shiga University of Medical Science, Otsu, Japan
- Education Center for Medicine and Nursing, Shiga University of Medical Science, Otsu, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yukie Hirahara
- Faculty of Nursing, Kansai Medical University, Hirakata, Japan
| | - Daijiro Yanagisawa
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Otsu, Japan
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Liu X, Duan S, Jin Y, Walker E, Tsao M, Jang JH, Chen Z, Singh AK, Cantrell KL, Ingolfsson HI, Buratto SK, Bowers MT. Computationally Designed Molecules Modulate ALS-Related Amyloidogenic TDP-43 307-319 Aggregation. ACS Chem Neurosci 2023; 14:4395-4408. [PMID: 38050862 DOI: 10.1021/acschemneuro.3c00582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
Abnormal cytosolic aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) is observed in multiple diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration, and Alzheimer's disease. Previous studies have shown that TDP-43307-319 located at the C-terminal of TDP-43 can form higher-order oligomers and fibrils. Of particular interest are the hexamers that adopt a cylindrin structure that has been strongly correlated to neurotoxicity. In this study, we use the joint pharmacophore space (JPS) model to identify and generate potential TDP-43 inhibitors. Five JPS-designed molecules are evaluated using both experimental and computational methods: ion mobility mass spectrometry, thioflavin T fluorescence assay, circular dichroism spectroscopy, atomic force microscopy, and molecular dynamics simulations. We found that all five molecules can prevent the amyloid fibril formation of TDP-43307-319, but their efficacy varies significantly. Furthermore, among the five molecules, [AC0101] is the most efficient in preventing the formation of higher-order oligomers and dissociating preformed higher-order oligomers. Molecular dynamics simulations show that [AC0101] both is the most flexible and forms the most hydrogen bonds with the TDP-43307-319 monomer. The JPS-designed molecules can insert themselves between the β-strands in the hexameric cylindrin structure of TDP-43307-319 and can open its structure. Possible mechanisms for JPS-designed molecules to inhibit and dissociate TDP-43307-319 oligomers on an atomistic scale are proposed.
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Affiliation(s)
- Xikun Liu
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Shuya Duan
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yingying Jin
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ethan Walker
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Michelle Tsao
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Joshua H Jang
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Ziying Chen
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ambuj K Singh
- Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Kristi Lazar Cantrell
- Department of Chemistry, Westmont College, Santa Barbara, California 93108, United States
| | - Helgi I Ingolfsson
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Steven K Buratto
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry & Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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Bae H, Kang MJ, Ha SW, Jeong DE, Lee K, Lim S, Min JY, Min KB. Association of plasma amyloid-β oligomerization with theta/beta ratio in older adults. Front Aging Neurosci 2023; 15:1291881. [PMID: 38106526 PMCID: PMC10722169 DOI: 10.3389/fnagi.2023.1291881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 12/19/2023] Open
Abstract
Background Oligomeric Aβ (OAβ) is a promising candidate marker for Alzheimer's disease (AD) diagnosis. Electroencephalography (EEG) is a potential tool for early detection of AD. Still, whether EEG power ratios, particularly the theta/alpha ratio (TAR) and theta/beta ratio (TBR), reflect Aβ burden-a primary mechanism underlying cognitive impairment and AD. This study investigated the association of TAR and TBR with amyloid burden in older adults based on MDS-OAβ levels. Methods 529 individuals (aged ≥60 years) were recruited. All participants underwent EEG (MINDD SCAN, Ybrain Inc., South Korea) and AlzOn™ test (PeopleBio Inc., Gyeonggi-do, Republic of Korea) for quantifying MDS-OAβ values in the plasma. EEG variables were log-transformed to normalize the data distribution. Using the MDS-OAβ cutoff value (0.78 ng/mL), all participants were classified into two groups: high MDS-OAβ and low MDS-OAβ. Results Participants with high MDS-OAβ levels had significantly higher TARs and TBRs than those with low MDS-OAβ levels. The log-transformed TBRs in the central lobe (β = 0.161, p = 0.0026), frontal lobe (β = 0.145, p = 0.0044), parietal lobe (β = 0.166, p = 0.0028), occipital lobe (β = 0.158, p = 0.0058), and temporal lobe (beta = 0.162, p = 0.0042) were significantly and positively associated with increases in MDS-OAβ levels. After adjusting for the Bonferroni correction, the TBRs in all lobe regions, except the occipital lobe, were significantly associated with increased MDS-OAβ levels. Conclusion We found a significant association of MDS-OAβ with TBR in older adults. This finding indicates that an increase in amyloid burden may be associated with an increase in the low-frequency band and a decrease in the relatively high-frequency band.
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Affiliation(s)
- Heewon Bae
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
- Department of Clinical Research Design and Evaluation, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Min Ju Kang
- Department of Neurology, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Sang-Won Ha
- Department of Neurology, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Da-Eun Jeong
- Department of Neurology, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Kiwon Lee
- Ybrain Research Institute, Seongnam-si, Republic of Korea
| | - Seungui Lim
- Ybrain Research Institute, Seongnam-si, Republic of Korea
| | - Jin-Young Min
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Kyoung-Bok Min
- Department of Preventive Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Medical Research Center, Institute of Health Policy and Management, Seoul National University, Seoul, Republic of Korea
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Maroli N. Aquaporin-4 Mediated Aggregation of Alzheimer's Amyloid β-Peptide. ACS Chem Neurosci 2023; 14:2683-2698. [PMID: 37486638 DOI: 10.1021/acschemneuro.3c00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Clearance of Alzheimer's amyloid oligomers from the brain is crucial for preventing cell toxicity. Dementia complications arise as a result of apoptosis, which is caused by peptide plaques on the lipid surface of cells. Here, we employed all-atom and coarse-grained molecular dynamics simulations to investigate the aggregation of amyloid peptides at the lipid surface and the role of aquaporin-4 (AQP4) in facilitating peptide clearance from astrocytes. The network of protein-protein interactions through text mining revealed that the expression of AQP4 and amyloid aggregation were strongly correlated. It has also been revealed that the role of aquaporins in the etiology of Alzheimer's disease involves several interconnected proteins and pathways. The nature of aggregation at the surface of the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer was revealed by the interaction of amyloid oligomers. The membrane-bound pore region of AQP4 interacts with the peptide and slows its aggregation. This interaction maintains the helical content of the peptide while lowering its toxicity at the lipid surface. The hydrophobicity of the peptide also decreased because of these interactions, which may help in the removal of the peptide from astrocytes. Long-term coarse-grained MD simulations demonstrated different features of oligomer aggregation at the surface and strong oligomer attraction to AQP4, which inhibited aggregation. Additionally, the water dynamics of aquaporins demonstrate how the selectivity filter is broken to disrupt water flow. Our findings also provide insight into the physiological alterations in brain tissue associated with Alzheimer's disease, including water retention and increased water flow in the CSF. Furthermore, in vitro thioflavin fluorescence spectroscopy revealed a slower aggregation of the peptide in the presence of AQP4.
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Affiliation(s)
- Nikhil Maroli
- Computational Biology Division, DRDO Center for Life Science, Bharathiar University Campus, Coimbatore 641046, Tamil Nadu, India
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Awasthi S, Ying C, Li J, Mayer M. Simultaneous Determination of the Size and Shape of Single α-Synuclein Oligomers in Solution. ACS Nano 2023. [PMID: 37327131 DOI: 10.1021/acsnano.3c01393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Soluble oligomers of amyloid-forming proteins are implicated as toxic species in the context of several neurodegenerative diseases. Since the size and shape of these oligomers influence their toxicity, their biophysical characterization is essential for a better understanding of the structure-toxicity relationship. Amyloid oligomers are difficult to characterize by conventional approaches due to their heterogeneity in size and shape, their dynamic aggregation process, and their low abundance. This work demonstrates that resistive pulse measurements using polymer-coated solid-state nanopores enable single-particle-level characterization of the size and shape of individual αSyn oligomers in solution within minutes. A comparison of the resulting size distribution with single-particle analysis by transmission electron microscopy and mass photometry reveals good agreement with superior resolution by nanopore-based characterization. Moreover, nanopore-based analysis has the capability to combine rapid size analysis with an approximation of the oligomer shape. Applying this shape approximation to putatively toxic oligomeric species that range in size from 18 ± 7 aggregated monomers (10S) to 29 ± 10 aggregated monomers (15S) and in concentration from picomolar to nanomolar revealed oligomer shapes that agree well with previous estimates by cryo-EM with the added advantage that nanopore-based analysis occurs rapidly, in solution, and has the potential to become a widely accessible technique.
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Affiliation(s)
- Saurabh Awasthi
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Cuifeng Ying
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Jiali Li
- University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
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Saha D, Jana B. Identifying the Template for Oligomer to Fibril Conversion for Amyloid-β (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics. Chemphyschem 2022; 23:e202200393. [PMID: 36052514 DOI: 10.1002/cphc.202200393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/26/2022] [Indexed: 01/04/2023]
Abstract
The toxicity of amyloid-β (Aβ) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aβ aggregates. In this study, we investigate Aβ13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aβ13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel β-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the β-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aβ42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.
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Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
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Vu KHP, Blankenburg GH, Lesser-Rojas L, Chou CF. Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers. Molecules 2022; 27:6448. [PMID: 36234985 DOI: 10.3390/molecules27196448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Amyloid oligomeric species, formed during misfolding processes, are believed to play a major role in neurodegenerative and metabolic diseases. Deepening the knowledge about the structure of amyloid intermediates and their aggregation pathways is essential in understanding the underlying mechanisms of misfolding and cytotoxicity. However, structural investigations are challenging due to the low abundance and heterogeneity of those metastable intermediate species. Single-molecule techniques have the potential to overcome these difficulties. This review aims to report some of the recent advances and applications of vibrational spectroscopic techniques for the structural analysis of amyloid oligomers, with special focus on single-molecule studies.
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Gray ALH, Sawaya MR, Acharyya D, Lou J, Edington EM, Best MD, Prosser RA, Eisenberg DS, Do TD. Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices. Protein Sci 2022; 31:716-727. [PMID: 34954854 PMCID: PMC8862425 DOI: 10.1002/pro.4268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022]
Abstract
Atomic structures of amyloid oligomers that capture the neurodegenerative disease pathology are essential to understand disease-state causes and finding cures. Here we investigate the G6W mutation of the cytotoxic, hexameric amyloid model KV11. The mutation results into an asymmetric dodecamer composed of a pair of 30° twisted antiparallel β-sheets. The complete break between adjacent β-strands is unprecedented among amyloid fibril crystal structures and supports that our structure is an oligomer. The poor shape complementarity between mated sheets reveals an interior channel for binding lipids, suggesting that the toxicity may be due to a perturbation of lipid transport rather than a direct disruption of membrane integrity. Viability assays on mouse suprachiasmatic nucleus, anterior hypothalamus, and cerebral cortex demonstrated selective regional vulnerability consistent with Alzheimer's disease. Neuropeptides released from the brain slices may provide clues to how G6W initiates cellular injury.
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Affiliation(s)
- Amber L. H. Gray
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Michael R. Sawaya
- HHMIUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Biological ChemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Energy Institute for Genomics and ProteomicsUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Debalina Acharyya
- Department of Biochemistry & Cellular and Molecular BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Jinchao Lou
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | | | - Michael D. Best
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Rebecca A. Prosser
- Department of Biochemistry & Cellular and Molecular BiologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - David S. Eisenberg
- HHMIUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Biological ChemistryUniversity of CaliforniaLos AngelesCaliforniaUSA,Molecular Biology InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA,Department of Energy Institute for Genomics and ProteomicsUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Thanh D. Do
- Department of ChemistryUniversity of TennesseeKnoxvilleTennesseeUSA
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Firouzi R, Noohi B. Identification of key stabilizing interactions of amyloid-β oligomers based on fragment molecular orbital calculations on macrocyclic β-hairpin peptides. Proteins 2021; 90:229-238. [PMID: 34387401 DOI: 10.1002/prot.26212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 11/10/2022]
Abstract
Analyzing the electronic states and inter-/intra-molecular interactions of amyloid oligomers expand our understanding of the molecular basis of Alzheimer's disease and other amyloid diseases. In the current study, several high-resolution crystal structures of oligomeric assemblies of Aβ-derived peptides have been studied by the ab initio fragment molecular orbital (FMO) method. The FMO method provides comprehensive details of the molecular interactions between the residues of the amyloid oligomers at the quantum mechanical level. Based on the calculations, two sequential aromatic residues (F19 and F20) and negatively charged E22 on the central region of Aβ have been identified as key residues in oligomer stabilization and potential interesting pharmacophores for preventing oligomer formation.
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Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Bahare Noohi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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Yang J, Perrett S, Wu S. Single Molecule Characterization of Amyloid Oligomers. Molecules 2021; 26:948. [PMID: 33670093 DOI: 10.3390/molecules26040948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
The misfolding and aggregation of polypeptide chains into β-sheet-rich amyloid fibrils is associated with a wide range of neurodegenerative diseases. Growing evidence indicates that the oligomeric intermediates populated in the early stages of amyloid formation rather than the mature fibrils are responsible for the cytotoxicity and pathology and are potentially therapeutic targets. However, due to the low-populated, transient, and heterogeneous nature of amyloid oligomers, they are hard to characterize by conventional bulk methods. The development of single molecule approaches provides a powerful toolkit for investigating these oligomeric intermediates as well as the complex process of amyloid aggregation at molecular resolution. In this review, we present an overview of recent progress in characterizing the oligomerization of amyloid proteins by single molecule fluorescence techniques, including single-molecule Förster resonance energy transfer (smFRET), fluorescence correlation spectroscopy (FCS), single-molecule photobleaching and super-resolution optical imaging. We discuss how these techniques have been applied to investigate the different aspects of amyloid oligomers and facilitate understanding of the mechanism of amyloid aggregation.
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Abstract
One of the major components of the staphylococcal biofilm is surface proteins that assemble as scaffold components of the biofilm matrix. Among the different surface proteins able to contribute to biofilm formation, this review is dedicated to the Biofilm Associated Protein (Bap). Bap is part of the accessory genome of Staphylococcus aureus but orthologs of Bap in other staphylococcal species belong to the core genome. When present, Bap promotes adhesion to abiotic surfaces and induces strong intercellular adhesion by self-assembling into amyloid like aggregates in response to the levels of calcium and the pH in the environment. During infection, Bap enhances the adhesion to epithelial cells where it binds directly to the host receptor Gp96 and inhibits the entry of the bacteria into the cells. To perform such diverse range of functions, Bap comprises several domains, and some of them include several motifs associated to distinct functions. Based on the knowledge accumulated with the Bap protein of S. aureus, this review aims to summarize the current knowledge of the structure and properties of each domain of Bap and their contribution to Bap functionality.
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Affiliation(s)
- Jaione Valle
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, Mutilva, Spain
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
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Abushakra S, Porsteinsson AP, Sabbagh M, Bracoud L, Schaerer J, Power A, Hey JA, Scott D, Suhy J, Tolar M. APOE ε4/ε4 homozygotes with early Alzheimer's disease show accelerated hippocampal atrophy and cortical thinning that correlates with cognitive decline. Alzheimers Dement (N Y) 2020; 6:e12117. [PMID: 33304988 PMCID: PMC7716452 DOI: 10.1002/trc2.12117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Hippocampal volume (HV) and cortical thickness are commonly used imaging biomarkers in Alzheimer's disease (AD) trials, and may have utility as selection criteria for enrichment strategies. Atrophy rates of these measures, in the high-risk apolipoprotein E (APOE) ε4/ε4 homozygous AD subjects are unknown. METHODS Data from Alzheimer's Disease Neuroimaging Initiative (ADNI-1) and a tramiprosate trial were analyzed in APOE ε4/ε4 and APOE ε3/ε3 subjects with mild cognitive impairment (MCI) or mild AD. Magnetic resonance imaging (MRI) data were centrally processed using FreeSurfer; total HV and composite average cortical thickness were derived and adjusted for age, head size, and education. Volumetric changes from baseline were assessed using Boundary Shift Integral, and correlated with cognitive changes. RESULTS APOE ε4/ε4 MCI subjects showed significantly higher % HV atrophy and cortical thinning at 12 months (4.4%, 3.1%, n = 29) compared to APOE ε3/ε3 subjects (2.8%, 1.8%, n = 93) and similarly in mild AD (7.4%, 4.7% n = 21 vs 5.4%, 3.3% n = 29). Differences were all significant at 24 months. Over 24 months, HV atrophy and cortical thinning correlated significantly with Alzheimer's Disease Assessment Scale-Cognitive subscale worsening in APOE ε4/ε4 MCI subjects, but not in mild AD. DISCUSSION Correlation of volumetric measures to cognitive change in APOE ε4/ε4 subjects with early AD supports their role as efficacy biomarkers. If confirmed in a Phase 3 trial with ALZ-801 (pro-drug of tramiprosate) in APOE ε4/ε4 early AD subjects, it may allow their use as surrogate outcomes in future treatment or prevention trials in AD.
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Affiliation(s)
| | - Anton P. Porsteinsson
- Alzheimer's Disease CareResearch and Education ProgramUniversity of RochesterRochesterNew YorkUSA
| | - Marwan Sabbagh
- Cleveland Clinic Lou Ruvo Center for Brain Health & University of NevadaLas VegasNevadaUSA
| | | | | | | | | | | | - Joyce Suhy
- BioclinicaLyonFrance
- BioclinicaNewarkCaliforniaUSA
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14
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Rudajev V, Novotny J. The Role of Lipid Environment in Ganglioside GM1-Induced Amyloid β Aggregation. Membranes (Basel) 2020; 10:membranes10090226. [PMID: 32916822 PMCID: PMC7558528 DOI: 10.3390/membranes10090226] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 01/14/2023]
Abstract
Ganglioside GM1 is the most common brain ganglioside enriched in plasma membrane regions known as lipid rafts or membrane microdomains. GM1 participates in many modulatory and communication functions associated with the development, differentiation, and protection of neuronal tissue. It has, however, been demonstrated that GM1 plays a negative role in the pathophysiology of Alzheimer's disease (AD). The two features of AD are the formation of intracellular neurofibrillary bodies and the accumulation of extracellular amyloid β (Aβ). Aβ is a peptide characterized by intrinsic conformational flexibility. Depending on its partners, Aβ can adopt different spatial arrangements. GM1 has been shown to induce specific changes in the spatial organization of Aβ, which lead to enhanced peptide accumulation and deleterious effect especially on neuronal membranes containing clusters of this ganglioside. Changes in GM1 levels and distribution during the development of AD may contribute to the aggravation of the disease.
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15
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Findley CA, Bartke A, Hascup KN, Hascup ER. Amyloid Beta-Related Alterations to Glutamate Signaling Dynamics During Alzheimer's Disease Progression. ASN Neuro 2020; 11:1759091419855541. [PMID: 31213067 PMCID: PMC6582288 DOI: 10.1177/1759091419855541] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Alzheimer’s disease (AD) ranks sixth on the Centers for Disease Control and Prevention Top 10 Leading Causes of Death list for 2016, and the Alzheimer’s Association attributes 60% to 80% of dementia cases as AD related. AD pathology hallmarks include accumulation of senile plaques and neurofibrillary tangles; however, evidence supports that soluble amyloid beta (Aβ), rather than insoluble plaques, may instigate synaptic failure. Soluble Aβ accumulation results in depression of long-term potentiation leading to cognitive deficits commonly characterized in AD. The mechanisms through which Aβ incites cognitive decline have been extensively explored, with a growing body of evidence pointing to modulation of the glutamatergic system. The period of glutamatergic hypoactivation observed alongside long-term potentiation depression and cognitive deficits in later disease stages may be the consequence of a preceding period of increased glutamatergic activity. This review will explore the Aβ-related changes to the tripartite glutamate synapse resulting in altered cell signaling throughout disease progression, ultimately culminating in oxidative stress, synaptic dysfunction, and neuronal loss.
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Affiliation(s)
- Caleigh A Findley
- 1 Department of Neurology, Center for Alzheimer's Disease and Related Disorders, Neuroscience Institute, Southern Illinois University School of Medicine, Springfield, IL, USA.,2 Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Andrzej Bartke
- 3 Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Kevin N Hascup
- 1 Department of Neurology, Center for Alzheimer's Disease and Related Disorders, Neuroscience Institute, Southern Illinois University School of Medicine, Springfield, IL, USA.,2 Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA.,4 Department of Molecular Biology, Microbiology & Biochemistry, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Erin R Hascup
- 1 Department of Neurology, Center for Alzheimer's Disease and Related Disorders, Neuroscience Institute, Southern Illinois University School of Medicine, Springfield, IL, USA.,2 Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
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16
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Abstract
Elucidating the molecular mechanisms in the development of such a devastating neurodegenerative disorder as Alzheimer's disease (AD) is currently one of the major challenges of molecular medicine. Evidence strongly suggests that the development of AD is due to the accumulation of amyloid β (Aβ) oligomers; therefore, understanding the molecular mechanisms defining the conversion of physiologically important monomers of Aβ proteins into neurotoxic oligomeric species is the key for the development of treatments and preventions of AD. However, these oligomers are unstable and unavailable for structural, physical, and chemical studies. We have recently developed a novel flexible nano array (FNA)-oligomer scaffold approach in which monomers tethered inside a flexible template can assemble spontaneously into oligomers with sizes defined by the number of tethered monomers. The FNA approach was tested on short decamer Aβ(14-23) peptides which were assembled into dimers and trimers. In this paper, we have extended our FNA technique for assembling full-length Aβ42 dimers. The FNA scaffold enabling the self-assembly of Aβ42 dimers from tethered monomeric species has been designed and the assembly of the dimers has been validated by AFM force spectroscopy experiments. Two major parameters of the force spectroscopy probing, the rupture forces and the rupture profiles, were obtained to prove the assembly of Aβ42 dimers. In addition, the FNA-Aβ42 dimers were used to probe Aβ42 trimers in the force spectroscopy experiments with the use of AFM tips functionalized with FNA-Aβ42 dimers and the surface with immobilized Aβ42 monomers. We found that the binding force for the Aβ42 trimer is higher than the dimer (75 ± 7 pN vs. 60 ± 3 pN) and the rupture pattern corresponds to a cooperative dissociation of the trimer. The rupture profiles for the dissociation of the Aβ42 dimers and trimers are proposed. Prospects for further extension of the FNA-based approach for probing of higher order oligomers of Aβ42 proteins are discussed.
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Affiliation(s)
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, United States
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17
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Sahoo BR, Bekier ME, Liu Z, Kocman V, Stoddard AK, Anantharamaiah GM, Nowick J, Fierke CA, Wang Y, Ramamoorthy A. Structural Interaction of Apolipoprotein A-I Mimetic Peptide with Amyloid-β Generates Toxic Hetero-oligomers. J Mol Biol 2019; 432:1020-1034. [PMID: 31866295 DOI: 10.1016/j.jmb.2019.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 01/21/2023]
Abstract
Apolipoproteins are involved in pathological conditions of Alzheimer's disease (AD), and it has been reported that truncated apolipoprotein fragments and β-amyloid (Aβ) peptides coexist as neurotoxic heteromers within the plaques. Therefore, it is important to investigate these complexes at the molecular level to better understand their properties and roles in the pathology of AD. Here, we present a mechanistic insight into such heteromerization using a structurally homologue apolipoprotein fragment of apoA-I (4F) complexed with Aβ(M1-42) and characterize their toxicity. The 4F peptide slows down the aggregation kinetics of Aβ(M1-42) by constraining its structural plasticity. NMR and CD experiments identified 4F-Aβ(M1-42) heteromers comprised of unstructured Aβ(M1-42) and helical 4F. A uniform two-fold reduction in 15N/1H NMR signal intensities of Aβ(M1-42) with no observable chemical shift perturbation indicated the formation of a large complex, which was further confirmed by diffusion NMR experiments. Microsecond-scale atomistic molecular dynamics simulations showed that 4F interaction with Aβ(M1-42) is electrostatically driven and induces unfolding of Aβ(M1-42). Neurotoxicity profiling of Aβ(M1-42) complexed with 4F confirms a significant reduction in cell viability and neurite growth. Thus, the molecular architecture of heteromerization between 4F and Aβ(M1-42) discovered in this study provides evidence toward our understanding of the role of apolipoproteins or their truncated fragments in exacerbating AD pathology.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Michael E Bekier
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Zichen Liu
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Vojc Kocman
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Andrea K Stoddard
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - G M Anantharamaiah
- Department of Medicine, University of Alabama at Birmingham Medical Center, Birmingham, AL, 35294, USA
| | - James Nowick
- Department of Chemistry, University of California-Irvine, Irvine, CA, 92697-2025, USA
| | - Carol A Fierke
- Department of Chemistry, University of Texas A&M, College Station, TX, 77843-3255, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA.
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18
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Singh P, Bhat R. Binding of Noradrenaline to Native and Intermediate States during the Fibrillation of α-Synuclein Leads to the Formation of Stable and Structured Cytotoxic Species. ACS Chem Neurosci 2019; 10:2741-2755. [PMID: 30917654 DOI: 10.1021/acschemneuro.8b00650] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Parkinson's disease is characterized by the deterioration of dopaminergic neurons of substantia nigra pars compacta along with a substantial loss of noradrenergic neurons of the locus coeruleus, which is the major source of noradrenaline (NA) in the brain. We have investigated the interaction of NA with α-synuclein (α-syn), the major protein constituent of Lewy bodies that are the pathological hallmark of Parkinson's disease (PD). It is expected that NA, like dopamine, could bind to α-syn and modulate its aggregation propensity and kinetics, which could also contribute to the onset of PD. We have, thus, evaluated the thermodynamic parameters of interaction of NA with α-syn monomer as well as species formed at different stages during its fibrillation pathway and have investigated the conformational and aggregation properties using various spectroscopic and calorimetric techniques. Binding isotherms of NA with α-syn species formed at different time points in the pathway have been observed to be exothermic in nature, suggesting hydrogen bonding interactions and weak affinity with binding constants in the millimolar range in all the cases. The interaction site of NA for α-syn was determined using Förster resonance energy transfer measurements that resulted in its binding in close proximity (23 Å) of an Alexa-labeled A90C mutant of α-syn. Docking studies further suggested binding of NA to the C-terminal as well as the non-amyloid-β component (NAC) region of α-syn. We have shown that α-syn oligomerization into sodium dodecyl sulfate resistant, higher-order, β-sheet-rich species is dependent on the oxidation of NA. Under non-reducing conditions, NA was also found to disaggregate the intermediates, populated during the fibrillation pathway, which are more cytotoxic compared to amyloid fibrils, as observed by 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide cytotoxicity assay using a human neuroblastoma cell line. On the basis of these and earlier data, we propose that NA-induced formation of α-syn oligomers may contribute to the progressive loss of the noradrenergic neuronal population and the pronounced Lewy body deposition observed in patients with PD.
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Affiliation(s)
- Priyanka Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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19
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Abstract
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The
molecular mechanism of protein aggregation is of both fundamental
and clinical importance as amyloid aggregates are linked to a number
of neurodegenerative disorders. Such protein aggregates include macroscopic
insoluble fibrils as well as small soluble oligomeric species. Time-dependent
resolution of these species is prerequisite for a detailed quantitative
understanding of protein aggregation; this remains challenging due
to the lack of methods for detecting and characterizing transient
and heterogeneous protein oligomers. Here we have used single molecule
fluorescence techniques combined with mechanistic modeling to study
the heparin-induced aggregation of the repeat region of tau, which
forms the core region of neurofibrillary tangles found in Alzheimer’s
disease. We distinguish several subpopulations of oligomers with different
stability and follow their evolution during aggregation reactions
as a function of temperature and concentration. Employment of techniques
from chemical kinetics reveals that the two largest populations are
structurally distinct from fibrils and are both kinetically and thermodynamically
unstable. The first population is in rapid exchange with monomers
and held together by electrostatic interactions; the second is kinetically
more stable, dominates at later times, and is probably off-pathway
to fibril formation. These more stable oligomers may contribute to
other oligomer induced effects in the cellular environment, for example,
by overloading protein quality control systems. We also show that
the shortest growing filaments remain suspended in aqueous buffer
and thus comprise a third, smaller population of transient oligomers
with cross-β structure. Overall our data show that a diverse
population of oligomers of different structures and half-lives are
formed during the aggregation reaction with the great majority of
oligomers formed not going on to form fibrils.
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Affiliation(s)
- Magnus Kjaergaard
- Department of Chemistry, Cambridge University, Lensfield Rd, Cambridge CB2 1EW, United Kingdom
- Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
| | - Alexander J. Dear
- Department of Chemistry, Cambridge University, Lensfield Rd, Cambridge CB2 1EW, United Kingdom
| | - Franziska Kundel
- Department of Chemistry, Cambridge University, Lensfield Rd, Cambridge CB2 1EW, United Kingdom
| | - Seema Qamar
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Georg Meisl
- Department of Chemistry, Cambridge University, Lensfield Rd, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry, Cambridge University, Lensfield Rd, Cambridge CB2 1EW, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - David Klenerman
- Department of Chemistry, Cambridge University, Lensfield Rd, Cambridge CB2 1EW, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge CB2 0XY, United Kingdom
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20
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Abstract
A major feature of Alzheimer's disease (AD) pathology is the plaque composed of aggregated amyloid-β (Aβ) peptide. Although these plaques may have harmful properties, there is much evidence to implicate soluble oligomeric Aβ as the primary noxious form. Aβ oligomers can be generated both extracellularly and intracellularly. Aβ is toxic to neurons in a myriad of ways. It can cause pore formation resulting in the leakage of ions, disruption of cellular calcium balance, and loss of membrane potential. It can promote apoptosis, cause synaptic loss, and disrupt the cytoskeleton. Current treatments for AD are limited and palliative. Much research and effort is being devoted to reducing Aβ production as an approach to slowing or preventing the development of AD. Aβ formation results from the amyloidogenic cleavage of human amyloid precursor protein (APP). Reconfiguring this process to disfavor amyloid generation might be possible through the reduction of APP or inhibition of enzymes that convert the precursor protein to amyloid.
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Affiliation(s)
- Allison B Reiss
- Winthrop Research Institute, NYU Winthrop Hospital, 101 Mineola Boulevard, Mineola, NY 11501, USA
| | - Hirra A Arain
- Winthrop Research Institute, NYU Winthrop Hospital, 101 Mineola Boulevard, Mineola, NY 11501, USA
| | - Mark M Stecker
- Winthrop Research Institute, NYU Winthrop Hospital, 101 Mineola Boulevard, Mineola, NY 11501, USA
| | - Nicolle M Siegart
- Winthrop Research Institute, NYU Winthrop Hospital, 101 Mineola Boulevard, Mineola, NY 11501, USA
| | - Lora J Kasselman
- Winthrop Research Institute, NYU Winthrop Hospital, 101 Mineola Boulevard, Mineola, NY 11501, USA
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21
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Trumbore CN. Shear-Induced Amyloid Formation in the Brain: II. An Experimental System for Monitoring Amyloid Shear Processes and Investigating Potential Spinal Tap Problems. J Alzheimers Dis 2018; 59:543-557. [PMID: 28671126 PMCID: PMC5523842 DOI: 10.3233/jad-170259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Liquid sheared amyloid-β (Aβ) initiates amyloid cascade reactions, producing unstable, potentially toxic oligomers. There is a need for new analytical tools with which to study these oligomers. A very small bore capillary flow system is proposed as a tool for studying the effects of liquid shear in amyloid research. This simple system consists of injecting a short cylindrical liquid sample plug containing dissolved amyloid into a liquid mobile phase flowing through an empty, very small internal diameter capillary tube. For liquid samples containing a single protein sample, under conditions in which there is laminar flow and limited sample protein molecular diffusion, chromatograms monitoring the optical protein absorbance of capillary effluent contain either one or two peaks, depending on the mobile phase flow rate. By controlling the sample diffusion times through changes in flow rate and/or capillary diameter, this tool can be used to generate aliquot samples with precise, reproducible amounts of shear for exploring the effects of variable shear on amyloid systems. The tool can be used for producing in-capillary stopped flow spectra of shear-stressed Aβ monomers as well as for kinetic studies of Aβ dimer- and oligomer-forming reactions between shear stressed Aβ monomers. Many other experiments are suggested using this experimental tool for studying the effects of shear on different Aβ and other amyloid systems, including testing for potentially serious amyloid sampling errors in spinal tap quantitative analysis. The technique has potential as both a laboratory research and a clinical tool.
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Affiliation(s)
- Conrad N Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Kennett Square, PA, USA
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22
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Oropesa-Nuñez R, Seghezza S, Dante S, Diaspro A, Cascella R, Cecchi C, Stefani M, Chiti F, Canale C. Interaction of toxic and non-toxic HypF-N oligomers with lipid bilayers investigated at high resolution with atomic force microscopy. Oncotarget 2018; 7:44991-45004. [PMID: 27391440 PMCID: PMC5216700 DOI: 10.18632/oncotarget.10449] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/26/2016] [Indexed: 11/25/2022] Open
Abstract
Protein misfolded oligomers are considered the most toxic species amongst those formed in the process of amyloid formation and the molecular basis of their toxicity, although not completely understood, is thought to originate from the interaction with the cellular membrane. Here, we sought to highlight the molecular determinants of oligomer-membrane interaction by atomic force microscopy. We monitored the interaction between multiphase supported lipid bilayers and two types of HypF-N oligomers displaying different structural features and cytotoxicities. By our approach we imaged with unprecedented resolution the ordered and disordered lipid phases of the bilayer and different oligomer structures interacting with either phase. We identified the oligomers and lipids responsible for toxicity and, more generally, we established the importance of the membrane lipid component in mediating oligomer toxicity. Our findings support the importance of GM1 ganglioside in mediating the oligomer-bilayer interaction and support a mechanism of oligomer cytotoxicity involving bilayer destabilization by globular oligomers within GM1-rich ordered raft regions rather than by annular oligomers in the surrounding disordered membrane domains.
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Affiliation(s)
- Reinier Oropesa-Nuñez
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy.,DIBRIS Department, University of Genova, Genova, Italy
| | - Silvia Seghezza
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Silvia Dante
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy
| | - Alberto Diaspro
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Physics, University of Genova, Genova, Italy
| | - Roberta Cascella
- Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences, University of Florence, Firenze, Italy
| | - Cristina Cecchi
- Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences, University of Florence, Firenze, Italy
| | - Massimo Stefani
- Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences, University of Florence, Firenze, Italy
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences, University of Florence, Firenze, Italy
| | - Claudio Canale
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genova, Italy
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23
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Avila-Vazquez MF, Altamirano-Bustamante NF, Altamirano-Bustamante MM. Amyloid Biomarkers in Conformational Diseases at Face Value: A Systematic Review. Molecules 2017; 23:molecules23010079. [PMID: 29286329 PMCID: PMC6017595 DOI: 10.3390/molecules23010079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/03/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022] Open
Abstract
Conformational diseases represent a new aspect of proteomic medicine where diagnostic and therapeutic paradigms are evolving. In this context, the early biomarkers for target cell failure (neurons, β-cells, etc.) represent a challenge to translational medicine and play a multidimensional role as biomarkers and potential therapeutic targets. This systematic review, which follows the PICO and Prisma methods, analyses this new-fangled multidimensionality, its strengths and limitations, and presents the future possibilities it opens up. The nuclear diagnosis methods are immunoassays: ELISA, immunodot, western blot, etc., while the therapeutic approach is focused on pharmaco- and molecular chaperones.
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Affiliation(s)
- Maria Fernanda Avila-Vazquez
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, IMSS, Mexico City 06720, Mexico.
- Health Department, Universidad Iberoamericana, Mexico City 01219, Mexico.
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24
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Banerjee S, Sun Z, Hayden EY, Teplow DB, Lyubchenko YL. Nanoscale Dynamics of Amyloid β-42 Oligomers As Revealed by High-Speed Atomic Force Microscopy. ACS Nano 2017; 11:12202-12209. [PMID: 29165985 PMCID: PMC5752618 DOI: 10.1021/acsnano.7b05434] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Amyloid β-protein (Aβ) oligomers are emerging as potent neurotoxic species in Alzheimer's disease pathogenesis. Detailed characterization of oligomer structure and dynamics is necessary to develop oligomer-specific therapeutic agents. However, oligomers exist transiently, which complicates their structural analysis. One approach to mitigate these problems has been photochemical cross-linking of native oligomers. In these states, the oligomers can be isolated and purified for physical and chemical studies. Here we characterized the structure of isolated cross-linked Aβ42 trimers, pentamers, and heptamers with atomic force microscopy (AFM) imaging and probed their dynamics in solution using time-lapse high-speed AFM. This technique enables visualization of the structural dynamics of the oligomers at nanometer resolution on a millisecond time scale. Results demonstrate that cross-linked pentamers and heptamers are very dynamic fluctuating between a compact single-globular and multiglobular assemblies. Trimers remain in their single-globular geometry that elongates adopting an ellipsoidal shape. Biological significance of oligomers dynamics is discussed.
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Affiliation(s)
- Siddhartha Banerjee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States
| | - Eric Y. Hayden
- Department of Neurology, David Geffen School of Medicine, and Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, CA 90095, United States
| | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine, and Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, CA 90095, United States
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States
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25
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Nagel-Steger L, Owen MC, Strodel B. An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations. Chembiochem 2016; 17:657-76. [PMID: 26910367 DOI: 10.1002/cbic.201500623] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 12/27/2022]
Abstract
The deposition of amyloid in brain tissue in the context of neurodegenerative diseases involves the formation of intermediate species-termed oligomers-of lower molecular mass and with structures that deviate from those of mature amyloid fibrils. Because these oligomers are thought to be primarily responsible for the subsequent disease pathogenesis, the elucidation of their structure is of enormous interest. Nevertheless, because of the high aggregation propensity and the polydispersity of oligomeric species formed by the proteins or peptides in question, the preparation of appropriate samples for high-resolution structural methods has proven to be rather difficult. This is why theoretical approaches have been of particular importance in gaining insights into possible oligomeric structures for some time. Only recently has it been possible to achieve some progress with regard to the experimentally based structural characterization of defined oligomeric species. Here we discuss how theory and experiment are used to determine oligomer structures and what can be done to improve the integration of the two disciplines.
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Affiliation(s)
- Luitgard Nagel-Steger
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany
| | - Michael C Owen
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany.
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26
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Lasagna-Reeves CA, Rousseaux MW, Guerrero-Muñoz MJ, Park J, Jafar-Nejad P, Richman R, Lu N, Sengupta U, Litvinchuk A, Orr HT, Kayed R, Zoghbi HY. A native interactor scaffolds and stabilizes toxic ATAXIN-1 oligomers in SCA1. eLife 2015; 4. [PMID: 25988806 PMCID: PMC4462648 DOI: 10.7554/elife.07558] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/18/2015] [Indexed: 01/01/2023] Open
Abstract
Recent studies indicate that soluble oligomers drive pathogenesis in several neurodegenerative proteinopathies, including Alzheimer and Parkinson disease. Curiously, the same conformational antibody recognizes different disease-related oligomers, despite the variations in clinical presentation and brain regions affected, suggesting that the oligomer structure might be responsible for toxicity. We investigated whether polyglutamine-expanded ATAXIN-1, the protein that underlies spinocerebellar ataxia type 1, forms toxic oligomers and, if so, what underlies their toxicity. We found that mutant ATXN1 does form oligomers and that oligomer levels correlate with disease progression in the Atxn1(154Q/+) mice. Moreover, oligomeric toxicity, stabilization and seeding require interaction with Capicua, which is expressed at greater ratios with respect to ATXN1 in the cerebellum than in less vulnerable brain regions. Thus, specific interactors, not merely oligomeric structure, drive pathogenesis and contribute to regional vulnerability. Identifying interactors that stabilize toxic oligomeric complexes could answer longstanding questions about the pathogenesis of other proteinopathies.
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Affiliation(s)
| | - Maxime Wc Rousseaux
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | | | - Jeehye Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Paymaan Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Ronald Richman
- Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
| | - Nan Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Urmi Sengupta
- Department of Neurology, University of Texas Medical Branch, Galveston, United States
| | - Alexandra Litvinchuk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Harry T Orr
- Institute for Translational Neuroscience, University of Minnesota, Minnesota, United States
| | - Rakez Kayed
- Department of Neurology, University of Texas Medical Branch, Galveston, United States
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, United States
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Diociaiuti M, Gaudiano MC, Malchiodi-Albedi F. The slowly aggregating salmon Calcitonin: a useful tool for the study of the amyloid oligomers structure and activity. Int J Mol Sci 2011; 12:9277-95. [PMID: 22272133 DOI: 10.3390/ijms12129277] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 11/17/2011] [Accepted: 11/24/2011] [Indexed: 12/30/2022] Open
Abstract
Amyloid proteins of different aminoacidic composition share the tendency to misfold and aggregate in a similar way, following common aggregation steps. The process includes the formation of dimers, trimers, and low molecular weight prefibrillar oligomers, characterized by the typical morphology of globules less than 10 nm diameter. The globules spontaneously form linear or annular structures and, eventually, mature fibers. The rate of this process depends on characteristics intrinsic to the different proteins and to environmental conditions (i.e., pH, ionic strength, solvent composition, temperature). In the case of neurodegenerative diseases, it is now generally agreed that the pathogenic aggregates are not the mature fibrils, but the intermediate, soluble oligomers. However, the molecular mechanism by which these oligomers trigger neuronal damage is still unclear. In particular, it is not clear if there is a peculiar structure at the basis of the neurotoxic effect and how this structure interacts with neurons. This review will focus on the results we obtained using salmon Calcitonin, an amyloid protein characterized by a very slow aggregation rate, which allowed us to closely monitor the aggregation process. We used it as a tool to investigate the characteristics of amyloid oligomers formation and their interactions with neuronal cells. Our results indicate that small globules of about 6 nm could be the responsible for the neurotoxic effects. Moreover, our data suggest that the rich content in lipid rafts of neuronal cell plasma membrane may render neurons particularly vulnerable to the amyloid protein toxic effect.
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Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disorder. Currently available therapies are symptomatic but do not alter underlying disease progression. Immunotherapeutic approaches such as anti Aβ peptide active vaccination trials have had limited success to date. Intravenous immunoblobulin (IVIg) is widely used in immune-mediated neurological disorders such myasthenia gravis and Guillain-Barre syndrome. These preparations have been obtained from the pooled plasma of healthy human donors and contain natural anti-amyloid antibodies and are well tolerated. A small pilot study of passive immunotherapy using IVIg has suggested cognitive improvement. A multicenter phase III trial is ongoing and will determine whether or not this treatment can ameliorate cognitive deficits in mild-to-moderate AD. Here, we briefly review the pathogenic role of amyloid and tau in AD, as well as immunotherapeutic efforts to date. We also summarize what is known about naturally occurring anti-Aβ and tau antibodies in IVIg with a view toward explaining potential mechanisms underlying their therapeutic effects.
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Affiliation(s)
- Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, TX, USA. ; Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA. ; Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
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