1
|
Pagano K, De Rosa L, Tomaselli S, Molinari H, D'Andrea LD, Ragona L. Characterizing the Oligomers Distribution along the Aggregation Pathway of Amyloid Aβ1-40 by NMR. Chemistry 2024; 30:e202400594. [PMID: 38712990 DOI: 10.1002/chem.202400594] [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: 02/13/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
This study delves into the early aggregation process of the Aβ1-40 amyloid peptide, elucidating the associated oligomers distribution. Motivated by the acknowledged role of small oligomers in the neurotoxic damage linked to Alzheimer's disease, we present an experimental protocol for preparing 26-O-acyl isoAβ1-40, a modified Aβ1-40 peptide facilitating rapid isomerization to the native amide form at neutral pH. This ensures seed-free solutions, minimizing experimental variability. Additionally, we demonstrate the efficacy of coupling NMR diffusion ordered spectroscopy (DOSY) with the Inverse Laplace Transform (ILT) reconstruction method, for effective characterization of early aggregation processes. This innovative approach efficiently maps oligomers distributions across a wide spectrum of initial peptide concentrations offering unique insights into the evolution of oligomers relative populations. As a proof of concept, we demonstrate the efficacy of our approach assessing the impact of Epigallocathechin gallate, a known remodeling agent of amyloid fibrils, on the oligomeric distributions of aggregated Aβ1-40. The DOSY-ILT proposed approach stands as a robust and discriminating asset, providing a powerful strategy for rapidly gaining insight into potential inhibitors' impact on the aggregation process.
Collapse
Affiliation(s)
- Katiuscia Pagano
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini CNR, Via Pietro Castellino 111, Napoli, Italy
| | - Simona Tomaselli
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Henriette Molinari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Luca Domenico D'Andrea
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, Via Mario Bianco, 9, Milano, Italy
| | - Laura Ragona
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| |
Collapse
|
2
|
Liu H, Cui Y, Zhao X, Wei L, Wang X, Shen N, Odom T, Li X, Lawless W, Karunarathne K, Muschol M, Guida W, Cao C, Ye L, Cai J. Helical sulfonyl-γ-AApeptides modulating Aβ oligomerization and cytotoxicity by recognizing Aβ helix. Proc Natl Acad Sci U S A 2024; 121:e2311733121. [PMID: 38285951 PMCID: PMC10861862 DOI: 10.1073/pnas.2311733121] [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: 07/11/2023] [Accepted: 12/10/2023] [Indexed: 01/31/2024] Open
Abstract
In contrast to prevalent strategies which make use of β-sheet mimetics to block Aβ fibrillar growth, in this study, we designed a series of sulfonyl-γ-AApeptide helices that targeted the crucial α-helix domain of Aβ13-26 and stabilized Aβ conformation to avoid forming the neurotoxic Aβ oligomeric β-sheets. Biophysical assays such as amyloid kinetics and TEM demonstrated that the Aβ oligomerization and fibrillation could be greatly prevented and even reversed in the presence of sulfonyl-γ-AApeptides in a sequence-specific and dose-dependent manner. The studies based on circular dichroism, Two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) spectra unambiguously suggested that the sulfonyl-γ-AApeptide Ab-6 could bind to the central region of Aβ42 and induce α-helix conformation in Aβ. Additionally, Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) was employed to rule out a colloidal mechanism of inhibitor and clearly supported the capability of Ab-6 for inhibiting the formation of Aβ aggregated forms. Furthermore, Ab-6 could rescue neuroblastoma cells by eradicating Aβ-mediated cytotoxicity even in the presence of pre-formed Aβ aggregates. The confocal microscopy demonstrated that Ab-6 could still specifically bind Aβ42 and colocalize into mitochondria in the cellular environment, suggesting the rescue of cell viability might be due to the protection of mitochondrial function otherwise impaired by Aβ42 aggregation. Taken together, our studies indicated that sulfonyl-γ-AApeptides as helical peptidomimetics could direct Aβ into the off-pathway helical secondary structure, thereby preventing the formation of Aβ oligomerization, fibrillation and rescuing Aβ induced cell cytotoxicity.
Collapse
Affiliation(s)
- Heng Liu
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Yunpeng Cui
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xue Zhao
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Lulu Wei
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xudong Wang
- Department of Molecular Biosciences, University of South Florida, Tampa, FL33620
| | - Ning Shen
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Timothy Odom
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xuming Li
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - William Lawless
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | | | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL33620
| | - Wayne Guida
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Chuanhai Cao
- Taneja College of Pharmacy, University of South Florida, Tampa, FL33612
| | - Libin Ye
- Department of Molecular Biosciences, University of South Florida, Tampa, FL33620
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL33620
| |
Collapse
|
3
|
Sahoo S, Pal T, Mondal S, Ghanta KP, Bandyopadhyay S. Conformational Properties of Aβ Peptide Oligomers in Aqueous Ionic Liquid Solution: Insights from Molecular Simulation Studies. J Phys Chem B 2023; 127:10960-10973. [PMID: 38091356 DOI: 10.1021/acs.jpcb.3c05490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Alzheimer's disease is a progressive irreversible neurological disorder with abnormal extracellular deposition of amyloid β (Aβ) peptides in the brain. We have carried out atomistic molecular dynamics simulations to investigate the size-dependent conformational properties of aggregated Aβ oligomers of different orders, namely, pentamer [O(5)], decamer [O(10)], and hexadecamer [O(16)] in aqueous solutions containing the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]). The calculations revealed reduced peptide conformational fluctuations in O(5) and O(10) in the presence of the IL. In contrast, the higher order oligomer [O(16)] has been found to exhibit greater structural distortion due to enhanced flexibilities of its peptide units in the presence of the IL. Based on the distributions of the solvent (water) and the cosolvent (IL) components, it is demonstrated that exchange of water by the IL ion pairs at the exterior surface of the oligomers primarily occurs beyond the first layer of surface-bound water molecules. Importantly, a reduced number of relatively weaker peptide salt bridges have been found in O(16) in binary water-IL solution as compared to the other two smaller-sized oligomers [O(5) and O(10)]. Such differential influence of the IL on peptide salt bridges results in less favorable binding free energies of peptide monomers to O(16), which leads to its greater structural distortion and reduced stability compared to those of O(5) and O(10).
Collapse
Affiliation(s)
- Subhadip Sahoo
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Tamisra Pal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Krishna Prasad Ghanta
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Jeon J, Yau WM, Tycko R. Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering. Nat Commun 2023; 14:2964. [PMID: 37221174 DOI: 10.1038/s41467-023-38494-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.
Collapse
Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland/National Institute of Standards and Technology, Rockville, MD, 20850, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| |
Collapse
|
6
|
Rezaei-Ghaleh N, Amininasab M, Giller K, Becker S. Familial Alzheimer's Disease-Related Mutations Differentially Alter Stability of Amyloid-Beta Aggregates. J Phys Chem Lett 2023; 14:1427-1435. [PMID: 36734539 PMCID: PMC9940190 DOI: 10.1021/acs.jpclett.2c03729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Amyloid-beta (Aβ) deposition as senile plaques is a pathological hallmark of Alzheimer's disease (AD). AD is characterized by a large level of heterogeneity in amyloid pathology, whose molecular origin is poorly understood. Here, we employ NMR spectroscopy and MD simulation at ambient and high pressures and investigate how AD-related mutations in Aβ peptide influence the stability of Aβ aggregates. The pressure-induced monomer dissociation from Aβ aggregates monitored by NMR demonstrated that the Iowa (D23N), Arctic (E22G), and Osaka (ΔE22) mutations altered the pressure stability of Aβ40 aggregates in distinct manners. While the NMR data of monomeric Aβ40 showed only small localized effects of mutations, the MD simulation of mutated Aβ fibrils revealed their distinct susceptibility to elevated pressure. Our data propose a structural basis for the distinct stability of various Aβ fibrils and highlights "stability" as a molecular property potentially contributing to the large heterogeneity of amyloid pathology in AD.
Collapse
Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Institute
of Physical Biology, Heinrich Heine University
Düsseldorf, D-40225 Düsseldorf, Germany
- Institute
of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, D-52428 Jülich, Germany
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Mehriar Amininasab
- Department
of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, 1417466191 Tehran, Iran
| | - Karin Giller
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Stefan Becker
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| |
Collapse
|
7
|
Pal T, Sahoo S, Prasad Ghanta K, Bandyopadhyay S. Computational Investigation of Conformational Fluctuations of Aβ42 Monomers in Aqueous Ionic Liquid Mixtures. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
8
|
Mamone S, Glöggler S, Becker S, Rezaei-Ghaleh N. Early Divergence in Misfolding Pathways of Amyloid-Beta Peptides. Chemphyschem 2021; 22:2158-2163. [PMID: 34355840 PMCID: PMC8596873 DOI: 10.1002/cphc.202100542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Indexed: 01/01/2023]
Abstract
The amyloid cascade hypothesis proposes that amyloid‐beta (Aβ) aggregation is the initial triggering event in Alzheimer's disease. Here, we utilize NMR spectroscopy and monitor the structural dynamics of two variants of Aβ, Aβ40 and Aβ42, as a function of temperature. Despite having identical amino acid sequence except for the two additional C‐terminal residues, Aβ42 has higher aggregation propensity than Aβ40. As revealed by the NMR data on dynamics, including backbone chemical shifts, intra‐methyl cross‐correlated relaxation rates and glycine‐based singlet‐states, the C‐terminal region of Aβ, especially the G33‐L34‐M35 segment, plays a particular role in the early steps of temperature‐induced Aβ aggregation. In Aβ42, the distinct dynamical behaviour of C‐terminal residues at higher temperatures is accompanied with marked changes in the backbone dynamics of residues V24‐K28. The distinctive role of the C‐terminal region of Aβ42 in the initiation of aggregation defines a target for the rational design of Aβ42 aggregation inhibitors.
Collapse
Affiliation(s)
- Salvatore Mamone
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold-Str. 3A, 37075, Göttingen, Germany
| | - Stefan Glöggler
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold-Str. 3A, 37075, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany.,Institute of Physical Biology, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| |
Collapse
|
9
|
Lee MC, Liao YH, Chen SH, Chen YR. Amyloid-β40 E22K fibril in familial Alzheimer's disease is more thermostable and susceptible to seeding. IUBMB Life 2021; 74:739-747. [PMID: 34724333 DOI: 10.1002/iub.2570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/25/2021] [Accepted: 10/10/2021] [Indexed: 11/11/2022]
Abstract
Alzheimer's disease (AD) is the most prevalent and devastating neurodegenerative disease occurred in the elderly. One of the pathogenic hallmarks is senile plaques composed of amyloid-β (Aβ) fibrils. Single mutations resided in Aβ were found in familial AD (FAD) patients that have early onset of the disease. The molecular details and properties of each FAD Aβ variants are still elusive. Here, we employed collective spectroscopic techniques to examine the properties of various Aβ40 fibrils. We generated fibrils of wild type (WT) and three FAD mutants on residue E22 including E22G, E22K, and E22Q. We monitored fibril formation by thioflavin T (ThT) assay, examined secondary structure by Fourier transform infrared and far-UV circular dichroism spectroscopy, imaged fibril morphology by transmission electron microscopy, and evaluated ThT-binding kinetics. In the thermal experiments, we found E22K fibrils resisted to high temperature and retained significant β-sheet content than the others. E22K fibril seeds after high-temperature treatment still possess the seeding property, whereas WT fibril seeds are disturbed after the treatment. Therefore, in this study we demonstrated the mutation at E22K increases the thermal stability and seeding function of amyloid fibrils.
Collapse
Affiliation(s)
- Ming-Che Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Hung Liao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Hui Chen
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| |
Collapse
|
10
|
Vemulapalli SB, Becker S, Griesinger C, Rezaei-Ghaleh N. Combined High-Pressure and Multiquantum NMR and Molecular Simulation Propose a Role for N-Terminal Salt Bridges in Amyloid-Beta. J Phys Chem Lett 2021; 12:9933-9939. [PMID: 34617758 PMCID: PMC8521524 DOI: 10.1021/acs.jpclett.1c02595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Several lines of evidence point to the important role of the N-terminal region of amyloid-beta (Aβ) peptide in its toxic aggregation in Alzheimer's disease (AD). It is known that charge-altering modifications such as Ser8 phosphorylation promote Aβ fibrillar aggregation. In this Letter, we combine high-pressure NMR, multiquantum chemical exchange saturation transfer (MQ-CEST) NMR, and microseconds-long molecular dynamics simulation and provide evidence of the presence of several salt bridges between Arg5 and its nearby negatively charged residues, in particular, Asp7 and Glu3. The presence of these salt bridges is correlated with less extended structures in the N-terminal region of Aβ. Through density functional theory calculations, we demonstrate how the introduction of negatively charged phosphoserine 8 influences the network of adjacent salt bridges in Aβ and favors more extended N-terminal structures. Our data propose a structural mechanism for the Ser8-phosphorylation-promoted Aβ aggregation and define the N-terminal salt bridges as potential targets for anti-AD drug design.
Collapse
Affiliation(s)
- Sahithya
Phani Babu Vemulapalli
- Department
of NMR-based Structural Biology, Max Planck
Institute for Biophysical Chemistry, Göttingen 37077, Germany
- Institute
for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg 26129, Germany
| | - Stefan Becker
- Department
of NMR-based Structural Biology, Max Planck
Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Christian Griesinger
- Department
of NMR-based Structural Biology, Max Planck
Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department
of NMR-based Structural Biology, Max Planck
Institute for Biophysical Chemistry, Göttingen 37077, Germany
- Department
of Neurology, University Medical Center
Göttingen, Göttingen 37075, Germany
- Institute
for Physical Biology, Heinrich Heine University, Düsseldorf 40225, Germany
| |
Collapse
|
11
|
Yamashita S, O Kamatari Y, Honda R, Niwa A, Tomiata H, Hara A, Kuwata K. Monomeric a-synuclein (aS) inhibits amyloidogenesis of human prion protein (hPrP) by forming a stable aS-hPrP hetero-dimer. Prion 2021; 15:37-43. [PMID: 33849375 PMCID: PMC8049198 DOI: 10.1080/19336896.2021.1910176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Intermolecular interaction between hPrP and αS was investigated using high-speed atomic force microscopy, dynamic light scattering, and nuclear magnetic resonance. We found that hPrP spontaneously gathered and naturally formed oligomers. Upon addition of monomer αS with a disordered conformation, poly-dispersive property of hPrP was lost, and hetero-dimer formation started quite coherently, and further oligomerization was not observed. Solution structure of hPrP-αS dimer was firstly characterized using hetero-nuclear NMR spectroscopy. In this hetero-dimeric complex, C-terminal helical region of hPrP was in the molten-globule like state, while specific sites including hot spot and C-terminal region of αS selectively interacted with hPrP. Thus αS may suppress amyloidogenesis of hPrP by trapping the hPrP intermediate by the formation of a stable hetero-dimer with hPrP. Abbreviations: hPrP, human prion protein of amino acid residues of 23-231; PrPC, cellular form of prion protein; PrPSc, scrapie form of prion protein, HS-AFM; high speed atomic force microscopy; αS, α-synuclein; DLS, dynamic light scattering
Collapse
Affiliation(s)
- Satoshi Yamashita
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan
| | - Yuji O Kamatari
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Gifu, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan
| | - Ayumi Niwa
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Tokai National Higher Education System, Gifu, Japan
| | - Hiroyuki Tomiata
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Tokai National Higher Education System, Gifu, Japan
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Tokai National Higher Education System, Gifu, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Tokai National Higher Education and Research System, Gifu, Japan.,Department of Gene and Development, Gifu University School of Medicine, Tokai National Higher Education and Research System, Gifu, Japan
| |
Collapse
|
12
|
Kakeshpour T, Ramanujam V, Barnes CA, Shen Y, Ying J, Bax A. A lowly populated, transient β-sheet structure in monomeric Aβ 1-42 identified by multinuclear NMR of chemical denaturation. Biophys Chem 2020; 270:106531. [PMID: 33453683 DOI: 10.1016/j.bpc.2020.106531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023]
Abstract
Chemical denaturation is a well-established approach for probing the equilibrium between folded and unfolded states of proteins. We demonstrate applicability of this method to the detection of a small population of a transiently folded structural element in a system that is often considered to be intrinsically fully disordered. The 1HN, 15N, 13Cα, and 13C' chemical shifts of Aβ1-40 and Aβ1-42 peptides and their M35-oxidized variants were monitored as a function of urea concentration and compared to analogous urea titrations of synthetic pentapeptides of homologous sequence. Fitting of the chemical shift titrations yields a 10 ± 1% population for a structured element at the C-terminus of Aβ1-42 that folds with a cooperativity of m = 0.06 kcal/mol·M. The fit also yields the chemical shifts of the folded state and, using a database search, for Aβ1-42 these shifts identified an antiparallel intramolecular β-sheet for residues I32-A42, linked by a type I' β-turn at G37 and G38. The structure is destabilized by oxidation of M35. Paramagnetic relaxation rates and two previously reported weak, medium-range NOE interactions are consistent with this transient β-sheet. Introduction of the requisite A42C mutation and tagging with MTSL resulted in a small stabilization of this β-sheet. Chemical shift analysis suggests a C-terminal β-sheet may be present in Aβ1-40 too, but the turn type at G37 is not type I'. The approach to derive Transient Structure from chemical Denaturation by NMR (TSD-NMR), demonstrated here for Aβ peptides, provides a sensitive tool for identifying the presence of lowly populated, transiently ordered elements in proteins that are considered to be intrinsically disordered, and permits extraction of structural data for such elements.
Collapse
Affiliation(s)
- Tayeb Kakeshpour
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Venkat Ramanujam
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - C Ashley Barnes
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
| |
Collapse
|
13
|
Tandem-Homodimer of a β-Sheet-Forming Short Peptide Inhibits Random-to-β Structural Transition of Its Original Monomer. Processes (Basel) 2020. [DOI: 10.3390/pr8111421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
There is an increasing interest in designing fibrillogenesis modulators for treating amyloid β (Aβ)-peptide-associated diseases. The use of Aβ fragment peptides and their derivatives, as well as nonpeptidyl natural products, is one promising approach to prevent Aβ fibrillation. In this study, we demonstrate that tandem-homodimers (TDs) of a β-sheet-forming short peptide in which the amino acid sequence is duplicated in series and joined via an amino alkanoic acid linker of different chain lengths, preventing the random-to-β structural transition of the original monomer. Ape5-TD, containing 5-amino pentanoate, most potently prevented this transition for at least five days by generating disordered aggregates with reduced tryptic stability. The linkers in the TDs generated this inhibitory activity, probably due to their bent conformations and hydrophobicity, appropriate for accommodating and twisting the monomers, resulting in irregular arrangements of the peptides. The present study could allow the design of a new class of protein/peptide fibrillogenesis modulators.
Collapse
|
14
|
Tavanti F, Pedone A, Menziani MC, Alexander-Katz A. Computational Insights into the Binding of Monolayer-Capped Gold Nanoparticles onto Amyloid-β Fibrils. ACS Chem Neurosci 2020; 11:3153-3160. [PMID: 32926781 DOI: 10.1021/acschemneuro.0c00497] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloids-β (Aβ) fibrils are involved in several neurodegenerative diseases. In this study, atomistic molecular dynamics simulations have been used to investigate how monolayer-protected gold nanoparticles interact with Aβ(1-40) and Aβ(1-42) fibrils. Our results show that small gold nanoparticles bind with the external side of amyloid-β fibrils that is involved in the fibrillation process. The binding affinity, studied for both kinds of fibrils as a function of the monolayer composition and the nanoparticle diameter, is modulated by hydrophobic interactions and ligand monolayer conformation. Our findings thus show that monolayer-protected nanoparticles are good candidates to prevent fibril aggregation and secondary nucleation or to deliver drugs to specific fibril regions.
Collapse
Affiliation(s)
- Francesco Tavanti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
- CNR-NANO Istituto Nanoscienze, Centro S3, Via Campi 213/A, I-41125 Modena, Italy
| | - Alfonso Pedone
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi, 103, I-41125 Modena, Italy
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Massachusetts Avenue, 77, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
15
|
Amyloidogenic Intrinsically Disordered Proteins: New Insights into Their Self-Assembly and Their Interaction with Membranes. Life (Basel) 2020; 10:life10080144. [PMID: 32784399 PMCID: PMC7459996 DOI: 10.3390/life10080144] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/02/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
Aβ, IAPP, α-synuclein, and prion proteins belong to the amyloidogenic intrinsically disordered proteins’ family; indeed, they lack well defined secondary and tertiary structures. It is generally acknowledged that they are involved, respectively, in Alzheimer’s, Type II Diabetes Mellitus, Parkinson’s, and Creutzfeldt–Jakob’s diseases. The molecular mechanism of toxicity is under intense debate, as many hypotheses concerning the involvement of the amyloid and the toxic oligomers have been proposed. However, the main role is represented by the interplay of protein and the cell membrane. Thus, the understanding of the interaction mechanism at the molecular level is crucial to shed light on the dynamics driving this phenomenon. There are plenty of factors influencing the interaction as mentioned above, however, the overall view is made trickier by the apparent irreproducibility and inconsistency of the data reported in the literature. Here, we contextualized this topic in a historical, and even more importantly, in a future perspective. We introduce two novel insights: the chemical equilibrium, always established in the aqueous phase between the free and the membrane phospholipids, as mediators of protein-transport into the core of the bilayer, and the symmetry-breaking of oligomeric aggregates forming an alternating array of partially ordered and disordered monomers.
Collapse
|
16
|
Bera S, Gayen N, Mohid SA, Bhattacharyya D, Krishnamoorthy J, Sarkar D, Choi J, Sahoo N, Mandal AK, Lee D, Bhunia A. Comparison of Synthetic Neuronal Model Membrane Mimics in Amyloid Aggregation at Atomic Resolution. ACS Chem Neurosci 2020; 11:1965-1977. [PMID: 32492332 DOI: 10.1021/acschemneuro.0c00166] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Alzheimer's disease (AD) is a severe neurodegenerative disorder caused by abnormal accumulation of toxic amyloid plaques of the amyloid-beta (Aβ) or the tau proteins in the brain. The plaque deposition leading to the collapse of the cellular integrity is responsible for a myriad of surface phenomena acting at the neuronal lipid interface. Recent years have witnessed dysfunction of the blood-brain barriers (BBB) associated with AD. Several studies support the idea that BBB acts as a platform for the formation of misfolded Aβ peptide, promoting oligomerization and fibrillation, compromising the overall integrity of the central nervous system. While the amyloid plaque deposition has been known to be responsible for the collapse of the BBB membrane integrity, the causal effect relationship between BBB and Aβ amyloidogenesis remains unclear. In this study, we have used physiologically relevant synthetic model membrane systems to gain atomic insight into the functional aspects of the lipid interface. Here, we have used a minimalist BBB mimic, POPC/POPG/cholesterol/GM1, to compare with the native BBB (total lipid brain extract (TLBE)), to understand the molecular events occurring in the membrane-induced Aβ40 amyloid aggregation. Our study showed that the two membrane models accelerated the Aβ40 aggregation kinetics with differential secondary structural transitions of the peptide. The observed structural transitions are defined by the lipid compositions, which in turn undermines the differences in lipid surface phenomena, leading to peptide induced cellular toxicity in the neuronal membrane.
Collapse
Affiliation(s)
- Swapna Bera
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Nilanjan Gayen
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Sk. Abdul Mohid
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | | | | | - Dibakar Sarkar
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Jihye Choi
- Department of Fine Chemistry & Convergence Institute of Biomedical and Biomaterials, Seoul National University of Science and Technology, Seoul 139-743, Korea
| | - Nirakar Sahoo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, Texas 78539, United States
| | - Atin K. Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - DongKuk Lee
- Department of Fine Chemistry & Convergence Institute of Biomedical and Biomaterials, Seoul National University of Science and Technology, Seoul 139-743, Korea
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| |
Collapse
|
17
|
Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
Collapse
Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| |
Collapse
|
18
|
Effect of aggregated Aβ protofilaments on intermolecular vibrational spectrum of confined water. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1699-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
19
|
Posado-Fernández A, Afonso CF, Dória G, Flores O, Cabrita EJ. Epitope Mapping by NMR of a Novel Anti-Aβ Antibody (STAB-MAb). Sci Rep 2019; 9:12241. [PMID: 31439854 PMCID: PMC6706428 DOI: 10.1038/s41598-019-47626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 07/19/2019] [Indexed: 11/17/2022] Open
Abstract
Alzheimer´s Disease (AD) is one of the most common neurodegenerative disorders worldwide. Excess of β-amyloid (Aβ), a peptide with a high propensity to misfold and self-aggregate, is believed to be the major contributor to the observed neuronal degeneration and cognitive decline in AD. Here, we characterize the epitope of a novel anti-Aβ monoclonal antibody, the STAB-MAb, which has previously demonstrated picomolar affinities for both monomers (KD = 80 pM) and fibrils (KD = 130 pM) of Aβ(1–42) and has shown therapeutic efficacy in preclinical mouse models of AD. Our findings reveal a widespread epitope that embraces several key Aβ residues that have been previously described as important in the Aβ fibrillation process. Of note, STAB-MAb exhibits a stronger affinity for the N-terminus of Aβ and stabilizes an α-helix conformation in the central to N-terminal region of the peptide, in addition to disrupting a characteristic salt-bridge of a hairpin structure present in fibrils. The NMR derived epitope supports the observed results from ThT-monitored fluorescence and electron microscopy experiments, in which STAB-MAb was shown to inhibit the formation of aggregates and promote disruption of pre-formed fibrils. In combination with the published in vitro and in vivo assays, our study highlights STAB-MAb as a rare and versatile antibody with analytical, diagnostic and therapeutic efficacy.
Collapse
Affiliation(s)
- Adrián Posado-Fernández
- UCIBIO, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-516, Caparica, Portugal.,STAB VIDA Lda., Madan Parque, Rua dos Inventores, 2825-182, Caparica, Portugal
| | - Cláudia F Afonso
- UCIBIO, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-516, Caparica, Portugal.,Instituto de Medicina Molecular (iMM), Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Gonçalo Dória
- STAB VIDA Lda., Madan Parque, Rua dos Inventores, 2825-182, Caparica, Portugal
| | - Orfeu Flores
- STAB VIDA Lda., Madan Parque, Rua dos Inventores, 2825-182, Caparica, Portugal
| | - Eurico J Cabrita
- UCIBIO, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-516, Caparica, Portugal.
| |
Collapse
|
20
|
Ghosh S, T D, Baul U, Vemparala S. Aggregation dynamics of charged peptides in water: Effect of salt concentration. J Chem Phys 2019; 151:074901. [DOI: 10.1063/1.5100890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Susmita Ghosh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Devanand T
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Upayan Baul
- Institue of Physics, Albert-Ludwigs-University of Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| |
Collapse
|
21
|
Nguyen HL, Krupa P, Hai NM, Linh HQ, Li MS. Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations. J Phys Chem B 2019; 123:7253-7269. [DOI: 10.1021/acs.jpcb.9b04208] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hoang Linh Nguyen
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software
City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Biomedical Engineering Department, Ho Chi Minh City University of Technology-VNU HCM, 268 Ly Thuong Kiet Street, Distr. 10, Ho Chi Minh City 700000, Vietnam
| | - Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Nguyen Minh Hai
- Faculty of Physics and Engineering Physics, University of Science-VNU HCM, Ho Chi Minh City 700000, Vietnam
| | - Huynh Quang Linh
- Biomedical Engineering Department, Ho Chi Minh City University of Technology-VNU HCM, 268 Ly Thuong Kiet Street, Distr. 10, Ho Chi Minh City 700000, Vietnam
| | - Mai Suan Li
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| |
Collapse
|
22
|
Owen MC, Gnutt D, Gao M, Wärmländer SKTS, Jarvet J, Gräslund A, Winter R, Ebbinghaus S, Strodel B. Effects of in vivo conditions on amyloid aggregation. Chem Soc Rev 2019; 48:3946-3996. [PMID: 31192324 DOI: 10.1039/c8cs00034d] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One of the grand challenges of biophysical chemistry is to understand the principles that govern protein misfolding and aggregation, which is a highly complex process that is sensitive to initial conditions, operates on a huge range of length- and timescales, and has products that range from protein dimers to macroscopic amyloid fibrils. Aberrant aggregation is associated with more than 25 diseases, which include Alzheimer's, Parkinson's, Huntington's, and type II diabetes. Amyloid aggregation has been extensively studied in the test tube, therefore under conditions that are far from physiological relevance. Hence, there is dire need to extend these investigations to in vivo conditions where amyloid formation is affected by a myriad of biochemical interactions. As a hallmark of neurodegenerative diseases, these interactions need to be understood in detail to develop novel therapeutic interventions, as millions of people globally suffer from neurodegenerative disorders and type II diabetes. The aim of this review is to document the progress in the research on amyloid formation from a physicochemical perspective with a special focus on the physiological factors influencing the aggregation of the amyloid-β peptide, the islet amyloid polypeptide, α-synuclein, and the hungingtin protein.
Collapse
Affiliation(s)
- Michael C Owen
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany and Lead Discovery Wuppertal, Bayer AG, 42096 Wuppertal, Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany and Sanofi-Aventis Deutschland GmbH, R&D, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 4a, 44227 Dortmund, Germany
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, 42525 Jülich, Germany. and Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| |
Collapse
|
23
|
Rezaei-Ghaleh N, Parigi G, Zweckstetter M. Reorientational Dynamics of Amyloid-β from NMR Spin Relaxation and Molecular Simulation. J Phys Chem Lett 2019; 10:3369-3375. [PMID: 31181936 PMCID: PMC6598774 DOI: 10.1021/acs.jpclett.9b01050] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer's disease. As an intrinsically disordered protein, Aβ undergoes extensive dynamics on multiple length and time scales. Access to a comprehensive picture of the reorientational dynamics in Aβ requires therefore the combination of complementary techniques. Here, we integrate 15N spin relaxation rates at three magnetic fields with microseconds-long molecular dynamics simulation, ensemble-based hydrodynamic calculations, and previously published nanosecond fluorescence correlation spectroscopy to investigate the reorientational dynamics of Aβ1-40 (Aβ40) at single-residue resolution. The integrative analysis shows that librational and dihedral angle fluctuations occurring at fast and intermediate time scales are not sufficient to decorrelate orientational memory in Aβ40. Instead, slow segmental motions occurring at ∼5 ns are detected throughout the Aβ40 sequence and reach up to ∼10 ns for selected residues. We propose that the modulation of time scales of reorientational dynamics with respect to intra- and intermolecular diffusion plays an important role in disease-related Aβ aggregation.
Collapse
Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Department
of Neurology, University Medical Center
Goettingen, 37075 Goettingen, Germany
- Department
for NMR-Based Structural Biology, Max Planck
Institute for Biophysical Chemistry, 37077 Goettingen, Germany
- E-mail:
| | - Giacomo Parigi
- Magnetic
Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Markus Zweckstetter
- Department
of Neurology, University Medical Center
Goettingen, 37075 Goettingen, Germany
- Department
for NMR-Based Structural Biology, Max Planck
Institute for Biophysical Chemistry, 37077 Goettingen, Germany
- Research
Group for Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Goettingen, Germany
| |
Collapse
|
24
|
Pilkington AW, Donohoe GC, Akhmedov NG, Ferrebee T, Valentine SJ, Legleiter J. Hydrogen Peroxide Modifies Aβ-Membrane Interactions with Implications for Aβ 40 Aggregation. Biochemistry 2019; 58:2893-2905. [PMID: 31187978 DOI: 10.1021/acs.biochem.9b00233] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) is pathologically characterized by the formation of extracellular senile plaques, predominately comprised of aggregated β-amyloid (Aβ), deposited in the brain. Aβ aggregation can result in a myriad of distinct aggregate species, from soluble oligomers to insoluble fibrils. Aβ strongly interacts with membranes, which can be linked to a variety of potential toxic mechanisms associated with AD. Oxidative damage accompanies the formation of Aβ aggregates, with a 10-50% proportion of Aβ aggregates being oxidized in vivo. Hydrogen peroxide (H2O2) is a reactive oxygen species implicated in a number of neurodegenerative diseases. Recent evidence has demonstrated that the H2O2 concentration fluctuates rapidly in the brain, resulting in large concentration spikes, especially in the synaptic cleft. Here, the impact of environmental H2O2 on Aβ aggregation in the presence and absence of lipid membranes is investigated. Aβ40 was exposed to H2O2, resulting in the selective oxidation of methionine 35 (Met35) to produce Aβ40Met35[O]. While oxidation mildly reduced the rate of Aβ aggregation and produced a distinct fibril morphology at high H2O2 concentrations, H2O2 had a much more pronounced impact on Aβ aggregation in the presence of total brain lipid extract vesicles. The impact of H2O2 on Aβ aggregation in the presence of lipids was associated with a reduced affinity of Aβ for the vesicle surface. However, this reduced vesicle affinity was predominately associated with lipid peroxidation rather than Aβ oxidation.
Collapse
Affiliation(s)
- Albert W Pilkington
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Gregory C Donohoe
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Novruz G Akhmedov
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Timothy Ferrebee
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Stephen J Valentine
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States.,Blanchette Rockefeller Neurosciences Institutes , West Virginia University , 1 Medical Center Drive , P.O. Box 9303, Morgantown , West Virginia 26505 , United States.,Department of Neuroscience , West Virginia University , 1 Medical Center Drive , P.O. Box 9303, Morgantown , West Virginia 26505 , United States
| |
Collapse
|
25
|
Mehrazma B, Rauk A. Exploring Amyloid-β Dimer Structure Using Molecular Dynamics Simulations. J Phys Chem A 2019; 123:4658-4670. [PMID: 31082235 DOI: 10.1021/acs.jpca.8b11251] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A major hallmark of Alzheimer's disease (AD) is the aggregation of amyloid-β peptides in the brains of people afflicted by the disease. The exact pathway to this catastrophic event is unknown. In this work, a total of 9.5 μs molecular dynamics simulations have been performed to investigate the structure and dynamics of the smallest form of toxic Aβ oligomers, i.e., the Aβ dimers. This study suggests that specific hydrophobic regions are vital in the aggregation process. Different possible structures for Aβ dimers are reported along with their relative binding affinity. These data may be used to design better Aβ-aggregation inhibitors. The diversity of the dimer structures suggests several aggregation pathways.
Collapse
Affiliation(s)
- Banafsheh Mehrazma
- Department of Chemistry , University of Calgary , Calgary AB , Canada T2N 1N4
| | - Arvi Rauk
- Department of Chemistry , University of Calgary , Calgary AB , Canada T2N 1N4
| |
Collapse
|
26
|
Blinov N, Wishart DS, Kovalenko A. Solvent Composition Effects on the Structural Properties of the Aβ42 Monomer from the 3D-RISM-KH Molecular Theory of Solvation. J Phys Chem B 2019; 123:2491-2506. [PMID: 30811210 DOI: 10.1021/acs.jpcb.9b00480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural characterization of amyloid (A)β peptides implicated in Alzheimer's disease is a challenging problem due to their intrinsically disordered nature and their high propensity for aggregation. Only limited information is currently available from experiments on conformational properties and aggregation pathways of the peptides in cellular environments. In silico modeling complements experimental information, providing atomistic insight into structure and dynamics of different Aβ species. All-atom explicit solvent molecular dynamics (MD) simulations with a properly selected force field can deliver reliable structural and dynamic information. In the case of intrinsically disordered Aβ peptides, enhanced sampling simulations beyond the nanosecond time scale are required to obtain statistically meaningful results even for simple solvent conditions. To overcome the challenges of conformational sampling in crowded cellular environments, alternative approaches have to be used, including postprocessing of MD data. In this study, we employ the statistical-mechanical, three-dimensional reference interaction site model with the Kovalenko-Hirata closure integral equation molecular theory of solvation to describe solvent composition effects on the conformational equilibrium in a structural ensemble of the Aβ42 (covering residues 1-42) monomer based on a statistical reweighting technique. The methodology enables a computationally efficient prediction on how different factors in the cellular environment, such as solvent composition, nonpolar solvation, and macromolecular crowding, affect the structural properties of the monomer. Similarities have been identified between changes in the structural ensemble caused by nonpolar solvation and crowded environments modeled by ionic solution with large negative ions. In particular, both solvent conditions reduce the random coil content and enhance the helical structure content of the monomer. In contrast to the previous studies, which reported increased α-helical content of peptides in crowded environments, this work attributes these structural features to the difference in solvent exposure of hydrophilic residues of the monomer for different secondary structure elements, rather than to (entropic) excluded volume effects.
Collapse
Affiliation(s)
- Nikolay Blinov
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
| | - David S Wishart
- Departments of Computing Science and Biological Sciences , University of Alberta , Edmonton , Alberta T6G 2E8 , Canada
| | - Andriy Kovalenko
- Department of Mechanical Engineering , Edmonton , Alberta T6G 1H9 , Canada.,Nanotechnology Research Centre , Edmonton , Alberta T6G 2M9 , Canada
| |
Collapse
|
27
|
Meng F, Bellaiche MMJ, Kim JY, Zerze GH, Best RB, Chung HS. Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation. Biophys J 2019; 114:870-884. [PMID: 29490247 DOI: 10.1016/j.bpj.2017.12.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/12/2017] [Accepted: 12/18/2017] [Indexed: 12/13/2022] Open
Abstract
Monomers of amyloid-β (Aβ) protein are known to be disordered, but there is considerable controversy over the existence of residual or transient conformations that can potentially promote oligomerization and fibril formation. We employed single-molecule Förster resonance energy transfer (FRET) spectroscopy with site-specific dye labeling using an unnatural amino acid and molecular dynamics simulations to investigate conformations and dynamics of Aβ isoforms with 40 (Aβ40) and 42 residues (Aβ42). The FRET efficiency distributions of both proteins measured in phosphate-buffered saline at room temperature show a single peak with very similar FRET efficiencies, indicating there is apparently only one state. 2D FRET efficiency-donor lifetime analysis reveals, however, that there is a broad distribution of rapidly interconverting conformations. Using nanosecond fluorescence correlation spectroscopy, we measured the timescale of the fluctuations between these conformations to be ∼35 ns, similar to that of disordered proteins. These results suggest that both Aβ40 and Aβ42 populate an ensemble of rapidly reconfiguring unfolded states, with no long-lived conformational state distinguishable from that of the disordered ensemble. To gain molecular-level insights into these observations, we performed molecular dynamics simulations with a force field optimized to describe disordered proteins. We find, as in experiments, that both peptides populate configurations consistent with random polymer chains, with the vast majority of conformations lacking significant secondary structure, giving rise to very similar ensemble-averaged FRET efficiencies.
Collapse
Affiliation(s)
- Fanjie Meng
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mathias M J Bellaiche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland; Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jae-Yeol Kim
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
| |
Collapse
|
28
|
Khatua P, Bandyopadhyay S. Dynamical crossover of water confined within the amphiphilic nanocores of aggregated amyloid β peptides. Phys Chem Chem Phys 2018; 20:14835-14845. [PMID: 29781021 DOI: 10.1039/c8cp01942h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It is believed that the self-assembly of amyloid beta (Aβ) peptides in the brain is the cause of Alzheimer's disease. Atomistic molecular dynamics simulations of aqueous solutions of Aβ protofilaments of different sizes at room temperature have been carried out to explore the dynamic properties of water confined within the core and at the exterior surface of the protofilaments. Attempts have been made to understand how the non-uniform distortion of the protofilaments associated with their structural crossover influences the diffusivity and the hydrogen bonding environment of the confined water molecules. In contrast to the homogeneous solvent dynamical environment at the exterior surface, the calculations revealed heterogeneously restricted motions of water confined within the distorted cores of the protofilaments. Importantly, it is demonstrated that the structural crossover of the aggregates observed for the decamer is associated with a dynamical transition of water confined within its core. A direct one-to-one correlation between the heterogeneously restricted core water motions and the kinetics of the breaking and formation of hydrogen bonds quantitatively demonstrated that a modified hydrogen bond arrangement within the cores of higher order Aβ protofilaments is the origin behind the crossover in core water mobility. A fraction of the water molecules forming short-lived water-water hydrogen bonds within the core of the crossover protofilament decamer are believed to diffuse away easily from the core and thus play a crucial role in further growth of the protofilament by facilitating the binding of new peptide monomers.
Collapse
Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India.
| | | |
Collapse
|
29
|
Khatua P, Bandyopadhyay S. Understanding the microscopic origin behind heterogeneous properties of water confined in and around A β17-42 protofilaments. J Chem Phys 2018; 149:065101. [PMID: 30111136 DOI: 10.1063/1.5040672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aggregation of amyloid beta (Aβ) peptides in the brain is responsible for one of the most devastating neurodegenerative diseases, namely, Alzheimer's disease. In this study, we have carried out atomistic molecular dynamics simulations to explore the effects of non-uniform structural distortions of Aβ17-42 pre-fibrillar aggregates of different sizes on the microscopic structure and ordering of water molecules confined within their amphiphilic nanocores. The calculations revealed non-uniform peptide-water interactions resulting in simultaneous existence of both highly ordered and disordered water molecules within the spatially heterogeneous confined environment of the protofilament cores. It is found that the high degree of ordering originates from a sizable fraction of doubly coordinated core water molecules, while the randomly oriented ones are those that are coordinated with three neighbors in their first coordination shells. Furthermore, it is quantitatively demonstrated that relative fractions of these two types of water molecules are correlated with the protofilament core topology and the degree of confinement within that. It is proposed that the ordered core waters are likely to stabilize the Aβ protofilaments by screening the residue charges and favoring water-mediated salt bridge formations, while the randomly oriented ones can drive further growth of the protofilaments by being displaced easily during the docking of additional peptides. In that way, both types of core water molecules can play equally important roles in controlling the growth and stability of the Aβ-aggregates.
Collapse
Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| |
Collapse
|
30
|
Cavini IA, Munte CE, Erlach MB, van Groen T, Kadish I, Zhang T, Ziehm T, Nagel-Steger L, Kutzsche J, Kremer W, Willbold D, Kalbitzer HR. Inhibition of amyloid Aβ aggregation by high pressures or specific d-enantiomeric peptides. Chem Commun (Camb) 2018. [PMID: 29537428 DOI: 10.1039/c8cc01458b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pressure can shift the polymer-monomer equilibrium of Aβ, increasing pressure first leads to a release of Aβ-monomers, surprisingly at pressures higher than 180 MPa repolymerization is induced. By high pressure NMR spectroscopy, differences of partial molar volumes ΔV0 and compressibility factors Δβ' of polymerization were determined at different temperatures. The d-enantiomeric peptides RD2 and RD2D3 bind to monomeric Aβ with affinities substantially higher than those determined for fibril formation. By reducing the Aβ concentration below the critical concentration for polymerization they inhibit the formation of toxic oligomers. Chemical shift perturbation allows the identification of the binding sites. The d-peptides are candidates for drugs preventing Alzheimer's disease. We show that RD2D3 has a positive effect on the cognitive behaviour of transgenic (APPSwDI) mice prone to Alzheimer's disease. The heterodimer complexes have a smaller Stokes radius than Aβ alone indicating the recognition of a more compact conformation of Aβ identified by high pressure NMR before.
Collapse
Affiliation(s)
- Italo A Cavini
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Shigemitsu Y, Hiroaki H. Common molecular pathogenesis of disease-related intrinsically disordered proteins revealed by NMR analysis. J Biochem 2018; 163:11-18. [PMID: 28992347 DOI: 10.1093/jb/mvx056] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/17/2017] [Indexed: 01/23/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) are either completely unstructured or contain large disordered regions in their native state; they have drawn much attention in the field of molecular pathology. Some of them substantially tend to form protein self-assemblies, such as toxic or non-toxic aggregates and fibrils, and have been postulated to relate to diseases. These disease-related IDPs include Aβ(1-42) [Alzheimer's disease (AD)], Tau (AD and tauopathy), α-synuclein (Parkinson's disease) and p53 (cancer). Several studies suggest that these aggregation and/or fibril formation processes are often initiated by transient conformational changes of the IDPs prior to protein self-assembly. Interestingly, the pathological molecular processes of these IDPs share multiple common features with those of protein misfolding diseases, such as transmissible spongiform encephalopathy (PrPsc) and AL-amyloidosis (VL-domain of γ-immunoglobulin). This review provides an overview of solution NMR techniques that can help analyse the early and transient events of conformational equilibrium of IDPs and folded proteins.
Collapse
Affiliation(s)
- Yoshiki Shigemitsu
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi 464-8601, Japan
| |
Collapse
|
32
|
Blinov N, Khorvash M, Wishart DS, Cashman NR, Kovalenko A. Initial Structural Models of the Aβ42 Dimer from Replica Exchange Molecular Dynamics Simulations. ACS OMEGA 2017; 2:7621-7636. [PMID: 31457321 PMCID: PMC6645216 DOI: 10.1021/acsomega.7b00805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/26/2017] [Indexed: 05/27/2023]
Abstract
Experimental characterization of the molecular structure of small amyloid (A)β oligomers that are currently considered as toxic agents in Alzheimer's disease is a formidably difficult task due to their transient nature and tendency to aggregate. Such structural information is of importance because it can help in developing diagnostics and an effective therapy for the disease. In this study, molecular simulations and protein-protein docking are employed to explore a possible connection between the structure of Aβ monomers and the properties of the intermonomer interface in the Aβ42 dimer. A structurally diverse ensemble of conformations of the monomer was sampled in microsecond timescale implicit solvent replica exchange molecular dynamics simulations. Representative structures with different solvent exposure of hydrophobic residues and secondary structure content were selected to build structural models of the dimer. Analysis of these models reveals that formation of an intramonomer salt bridge (SB) between Asp23 and Lys28 residues can prevent the building of a hydrophobic interface between the central hydrophobic clusters (CHCs) of monomers upon dimerization. This structural feature of the Aβ42 dimer is related to the difference in packing of hydrophobic residues in monomers with the Asp23-Lys28 SB in on and off states, in particular, to a lower propensity to form hydrophobic contacts between the CHC domain and C-terminal residues in monomers with a formed SB. These findings could have important implications for understanding the difference between aggregation pathways of Aβ monomers leading to neurotoxic oligomers or inert fibrillar structures.
Collapse
Affiliation(s)
- Nikolay Blinov
- Department
of Mechanical Engineering, University of
Alberta, Edmonton, Alberta T6G 1H9, Canada
- National
Institute for Nanotechnology, National Research
Council of Canada, Edmonton, Alberta T6G 2M9, Canada
| | - Massih Khorvash
- Department
of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - David S. Wishart
- Departments
of Computing Science and Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E8, Canada
| | - Neil R. Cashman
- Department
of Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Andriy Kovalenko
- Department
of Mechanical Engineering, University of
Alberta, Edmonton, Alberta T6G 1H9, Canada
- National
Institute for Nanotechnology, National Research
Council of Canada, Edmonton, Alberta T6G 2M9, Canada
| |
Collapse
|
33
|
Bacci M, Vymětal J, Mihajlovic M, Caflisch A, Vitalis A. Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. J Chem Theory Comput 2017; 13:5117-5130. [PMID: 28870064 DOI: 10.1021/acs.jctc.7b00662] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The growth of amyloid fibrils from Aβ1-42 peptide, one of the key pathogenic players in Alzheimer's disease, is believed to follow a nucleation-elongation mechanism. Fibril elongation is often described as a "dock-lock" procedure, where a disordered monomer adsorbs to an existing fibril in a relatively fast process (docking), followed by a slower conformational transition toward the ordered state of the template (locking). Here, we use molecular dynamics simulations of an ordered pentamer of Aβ42 at fully atomistic resolution, which includes solvent, to characterize the elongation process. We construct a Markov state model from an ensemble of short trajectories generated by an advanced sampling algorithm that efficiently diversifies a subset of the system without any bias forces. This subset corresponds to selected dihedral angles of the peptide chain at the fibril tip favored to be the fast growing one experimentally. From the network model, we extract distinct locking pathways covering time scales in the high microsecond regime. Slow steps are associated with the exchange of hydrophobic contacts, between nonnative and native intermolecular contacts as well as between intra- and intermolecular ones. The N-terminal segments, which are disordered in fibrils and typically considered inert, are able to shield the lateral interfaces of the pentamer. We conclude by discussing our findings in the context of a refined dock-lock model of Aβ fibril elongation, which involves structural disorder for more than one monomer at the growing tip.
Collapse
Affiliation(s)
- Marco Bacci
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jiří Vymětal
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Maja Mihajlovic
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| |
Collapse
|
34
|
Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
Collapse
Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
35
|
Khatua P, Sinha SK, Bandyopadhyay S. Size-Dependent Conformational Features of Aβ17–42 Protofilaments from Molecular Simulation Studies. J Chem Inf Model 2017; 57:2378-2392. [DOI: 10.1021/acs.jcim.7b00407] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prabir Khatua
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Sudipta Kumar Sinha
- Department
of Chemistry, Indian Institute of Technology Ropar, Ropar 140001, India
| | - Sanjoy Bandyopadhyay
- Molecular
Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| |
Collapse
|
36
|
Aleksis R, Oleskovs F, Jaudzems K, Pahnke J, Biverstål H. Structural studies of amyloid-β peptides: Unlocking the mechanism of aggregation and the associated toxicity. Biochimie 2017; 140:176-192. [PMID: 28751216 DOI: 10.1016/j.biochi.2017.07.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases worldwide. Formation of amyloid plaques consisting of amyloid-β peptides (Aβ) is one of the hallmarks of AD. Several lines of evidence have shown a correlation between the Aβ aggregation and the disease development. Extensive research has been conducted with the aim to reveal the structures of the neurotoxic Aβ aggregates. However, the exact structure of pathological aggregates and mechanism of the disease still remains elusive due to complexity of the occurring processes and instability of various disease-relevant Aβ species. In this article we review up-to-date structural knowledge about amyloid-β peptides, focusing on data acquired using solution and solid state NMR techniques. Furthermore, we discuss implications from these structural studies on the mechanisms of aggregation and neurotoxicity.
Collapse
Affiliation(s)
- Rihards Aleksis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia.
| | - Filips Oleskovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia
| | - Jens Pahnke
- Department of Neuro-/Pathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo (UiO) & Oslo University Hospital (OUS), Norway; LIED, University of Lübeck Uzl, Germany; Leibniz-Institute of Plant Biochemistry (IPB), Halle, Germany
| | - Henrik Biverstål
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia; Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
37
|
Zhang ZX, Hu ZW, Zhao DS, Chen YX, Li YM. Helices with Rational Residues Conduct Different Modulations towards Aβ Aggregation. CHEM LETT 2017. [DOI: 10.1246/cl.170229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Zheng-Xiao Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Zhi-Wen Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - De-Sheng Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
- Beijing Institute for Brain Disorders Center of Parkinson’s Disease, P. R. China
| |
Collapse
|
38
|
|
39
|
Abstract
A key molecular species in Alzheimer's disease (AD) is the Aβ42 alloform of Aβ peptide, which is dominant in the amyloid plaques deposited in the brains of AD patients. Recent studies have decisively demonstrated that the prefibrillar soluble oligomers are the neurotoxic culprits and are associated with the pathology of AD. Nascent Aβ42 is predominantly disordered but samples α-helical conformations covering residues 15-24 and 29-35 in the presence of micelles and structure-inducing solvents. In this report, a focused library of oligopyridylamide based α-helical mimetics was designed to target the central α-helix subdomain of Aβ (Aβ13-26). A tripyridylamide, ADH-41, was identified as one of the most potent antagonists of Aβ fibrillation. Amyloid-assembly kinetics, transmission electron microscopy (TEM), and atomic force microscopy (AFM) show that ADH-41 wholly suppresses the aggregation of Aβ at a substoichiometric dose. Dot blot and ELISA assays demonstrate the inhibition of the putative neurotoxic Aβ oligomers. ADH-41 targets Aβ in a sequence and structure-specific manner, as it did not have any effect on the aggregation of islet amyloid polypeptide (IAPP), a peptide which shares sequence similarity with Aβ. Spectroscopic studies using NMR and CD confirm induction of α-helicity in Aβ mediated by ADH-41. Calorimetric and fluorescence titrations yielded binding affinity in the low micromolar range. ADH-41 was also effective at inhibiting the seed-catalyzed aggregation of Aβ probably by modulating the Aβ conformation into a fiber incompetent structure. Overall, we speculate that ADH-41 directs Aβ into off-pathway structures, and thereby alters various solution based functions of Aβ. Cell-based assays to assess the effect of ADH-41 on Aβ are underway and will be presented in due course.
Collapse
Affiliation(s)
- Sunil Kumar
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Andrew D Hamilton
- Department of Chemistry, New York University , New York, New York 10003, United States
| |
Collapse
|
40
|
Xiong N, Zhao Y, Dong X, Zheng J, Sun Y. Design of a Molecular Hybrid of Dual Peptide Inhibitors Coupled on AuNPs for Enhanced Inhibition of Amyloid β-Protein Aggregation and Cytotoxicity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1601666. [PMID: 28112856 DOI: 10.1002/smll.201601666] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 12/07/2016] [Indexed: 05/28/2023]
Abstract
Aggregation of amyloid-β protein (Aβ) is a pathological hallmark of Alzheimer's disease (AD), so the inhibition of Aβ aggregation is an important strategy for the prevention and treatment of AD. Herein, we proposed to design molecular hybrids of peptide inhibitors by combining two peptide inhibitors, VVIA and LPFFD, into single sequences and examined their effects on Aβ42 aggregation and cytotoxicity. The hybrid peptides exhibit increased but moderate inhibitory activity as compared to their two precursors. By conjugating the peptides onto gold nanoparticles (AuNPs), however, the inhibition activity of the corresponding peptide@AuNPs against Aβ42 aggregation and cytotoxicity is greatly improved. Among them, VVIACLPFFD (VCD10)@AuNP is the most effective, which increases cell viability from 48% to 82% at a dosage as low as 0.1 nmol L-1 (NPs) or 40 nmol L-1 (peptide). The superior capacity of VCD10@AuNPs is considered due to its branched dual-inhibitor sequence, and its special surface orientation and conformation. These structural features promote its synergetic interactions with Aβ on AuNP surface, leading to strong inhibitions of Aβ oligomerization and fibrillation and the cytotoxicity caused by the aggregation species. The findings suggest that potent inhibitors can be derived by hybridization of multiple peptide inhibitors with the hybrid products coupled onto nanoparticles.
Collapse
Affiliation(s)
- Neng Xiong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yanjiao Zhao
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
41
|
Lin TW, Chang CF, Chang YJ, Liao YH, Yu HM, Chen YR. Alzheimer's amyloid-β A2T variant and its N-terminal peptides inhibit amyloid-β fibrillization and rescue the induced cytotoxicity. PLoS One 2017; 12:e0174561. [PMID: 28362827 PMCID: PMC5376091 DOI: 10.1371/journal.pone.0174561] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/11/2017] [Indexed: 01/21/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common dementia affecting tens of million people worldwide. The primary neuropathological hallmark in AD is amyloid plaques composed of amyloid-β peptide (Aβ). Several familial mutations found in Aβ sequence result in early onset of AD. Previous studies showed that the mutations located at N-terminus of Aβ, such as the English (H6R) and Tottori (D7N) mutations, promote fibril formation and increase cytotoxicity. However, A2T mutant located at the very N-terminus of Aβ shows low-prevalence incidence of AD, whereas, another mutant A2V causes early onset of AD. To understand the molecular mechanism of the distinct effect and develop new potential therapeutic strategy, here, we examined the effect of full-length and N-terminal A2V/T variants to wild type (WT) Aβ40 by fibrillization assays and NMR studies. We found that full-length and N-terminal A2V accelerated WT fibrillization and induced large chemical shifts on the N-terminus of WT Aβ, whereas, full-length and N-terminal A2T retarded the fibrillization. We further examined the inhibition effect of various N-terminal fragments (NTFs) of A2T to WT Aβ. The A2T NTFs ranging from residue 1 to residue 7 to 10, but not 1 to 6 or shorter, are capable to retard WT Aβ fibrillization and rescue cytotoxicity. The results suggest that in the presence of full-length or specific N-terminal A2T can retard Aβ aggregation and the A2T NTFs can mitigate its toxicity. Our results provide a novel targeting site for future therapeutic development of AD.
Collapse
Affiliation(s)
- Tien-Wei Lin
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Jen Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hung Liao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hui-Ming Yu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
42
|
Urbanc B. Flexible N‐Termini of Amyloid β‐Protein Oligomers: A Link between Structure and Activity? Isr J Chem 2017. [DOI: 10.1002/ijch.201600097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Brigita Urbanc
- Department of Physics Drexel University Philadelphia, PA 19104 USA
- Faculty of Mathematics and Physics Jadranska ulica 19 1000 Ljubljana Slovenia
| |
Collapse
|
43
|
Wallin C, Kulkarni YS, Abelein A, Jarvet J, Liao Q, Strodel B, Olsson L, Luo J, Abrahams JP, Sholts SB, Roos PM, Kamerlin SCL, Gräslund A, Wärmländer SKTS. Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer's disease. J Trace Elem Med Biol 2016; 38:183-193. [PMID: 27085215 DOI: 10.1016/j.jtemb.2016.03.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 03/17/2016] [Indexed: 12/28/2022]
Abstract
Growing evidence links neurodegenerative diseases to metal exposure. Aberrant metal ion concentrations have been noted in Alzheimer's disease (AD) brains, yet the role of metals in AD pathogenesis remains unresolved. A major factor in AD pathogenesis is considered to be aggregation of and amyloid formation by amyloid-β (Aβ) peptides. Previous studies have shown that Aβ displays specific binding to Cu(II) and Zn(II) ions, and such binding has been shown to modulate Aβ aggregation. Here, we use nuclear magnetic resonance (NMR) spectroscopy to show that Mn(II) ions also bind to the N-terminal part of the Aβ(1-40) peptide, with a weak binding affinity in the milli- to micromolar range. Circular dichroism (CD) spectroscopy, solid state atomic force microscopy (AFM), fluorescence spectroscopy, and molecular modeling suggest that the weak binding of Mn(II) to Aβ may not have a large effect on the peptide's aggregation into amyloid fibrils. However, identification of an additional metal ion displaying Aβ binding reveals more complex AD metal chemistry than has been previously considered in the literature.
Collapse
Affiliation(s)
- Cecilia Wallin
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Yashraj S Kulkarni
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 751 24 Uppsala, Sweden
| | - Axel Abelein
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; Department of Neurobiology, Care Sciences and Society (NVS), H1, Division of Neurogeriatrics, Karolinska Institutet, Novum Pl 5 14157 Huddinge, Stockholm, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; The National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
| | - Qinghua Liao
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich, 52425, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich, Jülich, 52425, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Lisa Olsson
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Jinghui Luo
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Jan Pieter Abrahams
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland; Laboratory of Biomolecular Research, Paul Scherrer Institute, Department of Biology and Chemistry, OFLC/102CH-5232 Villigen PSI, Switzerland
| | - Sabrina B Sholts
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden; Department of Anthropology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC 20013, USA
| | - Per M Roos
- Institute of Environmental Medicine, Karolinska Institutet, Nobels väg 13, 171 77 Stockholm, Sweden; Department of Clinical Physiology, Capio St.Göran Hospital, St.Göransplan 1, 112 19 Stockholm, Sweden
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, 751 24 Uppsala, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden.
| |
Collapse
|
44
|
Acharya S, Srivastava KR, Nagarajan S, Lapidus LJ. Monomer Dynamics of Alzheimer Peptides and Kinetic Control of Early Aggregation in Alzheimer's Disease. Chemphyschem 2016; 17:3470-3479. [PMID: 27490673 DOI: 10.1002/cphc.201600706] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 12/20/2022]
Abstract
The rate of reconfiguration-or intramolecular diffusion-of monomeric Alzheimer (Aβ) peptides is measured and, under conditions that aggregation is more likely, peptide diffusion slows down significantly, which allows bimolecular associations to be initiated. By using the method of Trp-Cys contact quenching, the rate of reconfiguration is observed to be about five times faster for Aβ40 , which aggregates slowly, than that for Aβ42 , which aggregates quickly. Furthermore, the rate of reconfiguration for Aβ42 speeds up at higher pH, which slows aggregation, and in the presence of the aggregation inhibitor curcumin. The measured reconfiguration rates are able to predict the early aggregation behavior of the Aβ peptide and provide a kinetic basis for why Aβ42 is more prone to aggregation than Aβ40 , despite a difference of only two amino acids.
Collapse
Affiliation(s)
- Srabasti Acharya
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd. Rm 4227, East Lansing, MI, 48824, USA
| | - Kinshuk R Srivastava
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd. Rm 4227, East Lansing, MI, 48824, USA
| | - Sureshbabu Nagarajan
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd. Rm 4227, East Lansing, MI, 48824, USA
| | - Lisa J Lapidus
- Department of Physics and Astronomy, Michigan State University, 567 Wilson Rd. Rm 4227, East Lansing, MI, 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
45
|
Paul TJ, Hoffmann Z, Wang C, Shanmugasundaram M, DeJoannis J, Shekhtman A, Lednev IK, Yadavalli VK, Prabhakar R. Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach. J Phys Chem Lett 2016; 7:2758-64. [PMID: 27387853 PMCID: PMC5956519 DOI: 10.1021/acs.jpclett.6b01066] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this combined experimental (deep ultraviolet resonance Raman (DUVRR) spectroscopy and atomic force microscopy (AFM)) and theoretical (molecular dynamics (MD) simulations and stress-strain (SS)) study, the structural and mechanical properties of amyloid beta (Aβ40) fibrils have been investigated. The DUVRR spectroscopy and AFM experiments confirmed the formation of linear, unbranched and β-sheet rich fibrils. The fibrils (Aβ40)n, formed using n monomers, were equilibrated using all-atom MD simulations. The structural properties such as β-sheet character, twist, interstrand distance, and periodicity of these fibrils were found to be in agreement with experimental measurements. Furthermore, Young's modulus (Y) = 4.2 GPa computed using SS calculations was supported by measured values of 1.79 ± 0.41 and 3.2 ± 0.8 GPa provided by two separate AFM experiments. These results revealed size dependence of structural and material properties of amyloid fibrils and show the utility of such combined experimental and theoretical studies in the design of precisely engineered biomaterials.
Collapse
Affiliation(s)
- Thomas J. Paul
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Zachary Hoffmann
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Congzhou Wang
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Maruda Shanmugasundaram
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Jason DeJoannis
- Dassault Systèmes BIOVIA, San Deigo, California 92121, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Igor K. Lednev
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Vamsi K. Yadavalli
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| |
Collapse
|
46
|
Vugmeyster L, Clark MA, Falconer IB, Ostrovsky D, Gantz D, Qiang W, Hoatson GL. Flexibility and Solvation of Amyloid-β Hydrophobic Core. J Biol Chem 2016; 291:18484-95. [PMID: 27402826 DOI: 10.1074/jbc.m116.740530] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibril deposits found in Alzheimer disease patients are composed of amyloid-β (Aβ) protein forming a number of hydrophobic interfaces that are believed to be mostly rigid. We have investigated the μs-ms time-scale dynamics of the intra-strand hydrophobic core and interfaces of the fibrils composed of Aβ1-40 protein. Using solid-state (2)H NMR line shape experiments performed on selectively deuterated methyl groups, we probed the 3-fold symmetric and 2-fold symmetric polymorphs of native Aβ as well as the protofibrils of D23N Iowa mutant, associated with an early onset of Alzheimer disease. The dynamics of the hydrophobic regions probed at Leu-17, Leu-34, Val-36, and Met-35 side chains were found to be very pronounced at all sites and in all polymorphs of Aβ, with methyl axis motions persisting down to 230-200 K for most of the sites. The dominant mode of motions is the rotameric side chain jumps, with the Met-35 displaying the most complex multi-modal behavior. There are distinct differences in the dynamics among the three protein variants, with the Val-36 site displaying the most variability. Solvation of the fibrils does not affect methyl group motions within the hydrophobic core of individual cross-β subunits but has a clear effect on the motions at the hydrophobic interface between the cross-β subunits, which is defined by Met-35 contacts. In particular, hydration activates transitions between additional rotameric states that are not sampled in the dry protein. Thus, these results support the existence of water-accessible cavity recently predicted by molecular dynamics simulations and suggested by cryo-EM studies.
Collapse
Affiliation(s)
| | | | | | | | - Donald Gantz
- Boston University School of Medicine, Boston, Massachusetts 02118
| | - Wei Qiang
- Binghamton University, Binghamton, New York 13902, and
| | - Gina L Hoatson
- College of William and Mary, Williamsburg, Virginia 23187
| |
Collapse
|
47
|
Beyer I, Rezaei-Ghaleh N, Klafki HW, Jahn O, Haußmann U, Wiltfang J, Zweckstetter M, Knölker HJ. Solid-Phase Synthesis and Characterization of N-Terminally Elongated Aβ-3-x -Peptides. Chemistry 2016; 22:8685-93. [PMID: 27167300 PMCID: PMC5084751 DOI: 10.1002/chem.201600892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 01/24/2023]
Abstract
In addition to the prototypic amyloid-β (Aβ) peptides Aβ1-40 and Aβ1-42 , several Aβ variants differing in their amino and carboxy termini have been described. Synthetic availability of an Aβ variant is often the key to study its role under physiological or pathological conditions. Herein, we report a protocol for the efficient solid-phase peptide synthesis of the N-terminally elongated Aβ-peptides Aβ-3-38 , Aβ-3-40 , and Aβ-3-42 . Biophysical characterization by NMR spectroscopy, CD spectroscopy, an aggregation assay, and electron microscopy revealed that all three peptides were prone to aggregation into amyloid fibrils. Immunoprecipitation, followed by mass spectrometry, indicated that Aβ-3-38 and Aβ-3-40 are generated by transfected cells even in the presence of a tripartite β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor. The elongated Aβ peptides starting at Val(-3) can be separated from N-terminally-truncated Aβ forms by high-resolution isoelectric-focusing techniques, despite virtually identical isoelectric points. The synthetic Aβ variants and the methods presented here are providing tools to advance our understanding of the potential roles of N-terminally elongated Aβ variants in Alzheimer's disease.
Collapse
Affiliation(s)
- Isaak Beyer
- Department Chemie, Technische Universität Dresden, Bergstrasse 66, 01069, Dresden, Germany
| | - Nasrollah Rezaei-Ghaleh
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Hans-Wolfgang Klafki
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-Universität, 37075, Göttingen, Germany
| | - Olaf Jahn
- Max Planck Institute for Experimental Medicine, Proteomics Group, 37075, Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, University of Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Ute Haußmann
- University of Duisburg-Essen, 45141, Essen, Germany
| | - Jens Wiltfang
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany. ,
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Georg-August-Universität, 37075, Göttingen, Germany. ,
| | - Markus Zweckstetter
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain, University Medical Center Göttingen, University of Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Hans-Joachim Knölker
- Department Chemie, Technische Universität Dresden, Bergstrasse 66, 01069, Dresden, Germany.
| |
Collapse
|
48
|
Rezaei-Ghaleh N, Kumar S, Walter J, Zweckstetter M. Phosphorylation Interferes with Maturation of Amyloid-β Fibrillar Structure in the N Terminus. J Biol Chem 2016; 291:16059-67. [PMID: 27252381 DOI: 10.1074/jbc.m116.728956] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 11/06/2022] Open
Abstract
Neurodegeneration is characterized by the ubiquitous presence of modifications in protein deposits. Despite their potential significance in the initiation and progression of neurodegenerative diseases, the effects of posttranslational modifications on the molecular properties of protein aggregates are largely unknown. Here, we study the Alzheimer disease-related amyloid-β (Aβ) peptide and investigate how phosphorylation at serine 8 affects the structure of Aβ aggregates. Serine 8 is shown to be located in a region of high conformational flexibility in monomeric Aβ, which upon phosphorylation undergoes changes in local conformational dynamics. Using hydrogen-deuterium exchange NMR and fluorescence quenching techniques, we demonstrate that Aβ phosphorylation at serine 8 causes structural changes in the N-terminal region of Aβ aggregates in favor of less compact conformations. Structural changes induced by serine 8 phosphorylation can provide a mechanistic link between phosphorylation and other biological events that involve the N-terminal region of Aβ aggregates. Our data therefore support an important role of posttranslational modifications in the structural polymorphism of amyloid aggregates and their modulatory effect on neurodegeneration.
Collapse
Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- From the German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Strasse 3a, 37075 Göttingen, Germany, Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany,
| | - Sathish Kumar
- Department of Neurology, University of Bonn, 53127 Bonn, Germany, and
| | - Jochen Walter
- Department of Neurology, University of Bonn, 53127 Bonn, Germany, and
| | - Markus Zweckstetter
- From the German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Strasse 3a, 37075 Göttingen, Germany, Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, Department of Neurology, University Medical Center, University of Göttingen, Göttingen, Waldweg 33, 37073 Göttingen, Germany
| |
Collapse
|
49
|
High-speed atomic force microscopy reveals structural dynamics of amyloid β1-42 aggregates. Proc Natl Acad Sci U S A 2016; 113:5835-40. [PMID: 27162352 DOI: 10.1073/pnas.1524807113] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aggregation of amyloidogenic proteins into insoluble amyloid fibrils is implicated in various neurodegenerative diseases. This process involves protein assembly into oligomeric intermediates and fibrils with highly polymorphic molecular structures. These structural differences may be responsible for different disease presentations. For this reason, elucidation of the structural features and assembly kinetics of amyloidogenic proteins has been an area of intense study. We report here the results of high-speed atomic force microscopy (HS-AFM) studies of fibril formation and elongation by the 42-residue form of the amyloid β-protein (Aβ1-42), a key pathogenetic agent of Alzheimer's disease. Our data demonstrate two different growth modes of Aβ1-42, one producing straight fibrils and the other producing spiral fibrils. Each mode depends on initial fibril nucleus structure, but switching from one growth mode to another was occasionally observed, suggesting that fibril end structure fluctuated between the two growth modes. This switching phenomenon was affected by buffer salt composition. Our findings indicate that polymorphism in fibril structure can occur after fibril nucleation and is affected by relatively modest changes in environmental conditions.
Collapse
|
50
|
Binding Patterns Associated Aß-HSP60 p458 Conjugate to HLA-DR-DRB Allele of Human in Alzheimer's Disease: An In Silico Approach. Interdiscip Sci 2016; 10:93-104. [PMID: 27106586 DOI: 10.1007/s12539-016-0170-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 12/29/2022]
Abstract
Alzheimer's disease (AD) is a complex, irreversible, progressive brain disorder, which diminishes memory in a slow pace and thinking skills; ranked third by experts. It is a complex disorder that involves numerous cellular and subcellular alterations. The pathogenesis of AD is still unknown, but for better understanding, we proposed an in silico analysis to find out the binding patterns associated with HSP60. Several experimental conclusions have been drawn to understand the actual mechanism behind the forming of aggregation due to misfolding. Protein misfolding disorder is experimentally identified by the accumulation of protein aggregates at the intracellular or extracellular region of brain that adversely affects the cell functioning by disrupting the connection between the cells and ultimately leading to cell death. To unravel the mystery behind the mechanism of AD through computational approach, the current proposal shows the designing of Aß-HSP60 p458 conjugate followed by secondary structure analysis, which is further targeted to HLA-DR-DRB allele of human. The antigenicity of Aß (1-42) peptide is the major concern in our study predicted through PVS server, which provides an insight into the immunogenic behavior of Aß peptide. The mechanism involved in the interaction of HSP60-Aß conjugate with HLA-DR-DRB allele considering the fact that Aß (1-42) is highly immunogenic in human and interactions evoked highly robust T-cell response through MHC class II binding predictions. It was assisted by molecular dynamics simulation of predicted HSP60 structure followed by validation through Ramachandran plot analysis and protein-protein interaction of Aß (1-42) with HSP60.
Collapse
|