1
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Jeacock K, Chappard A, Gallagher KJ, Mackay CL, Kilgour DPA, Horrocks MH, Kunath T, Clarke DJ. Determining the Location of the α-Synuclein Dimer Interface Using Native Top-Down Fragmentation and Isotope Depletion-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:847-856. [PMID: 36976861 PMCID: PMC10161212 DOI: 10.1021/jasms.2c00339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
α-Synuclein (αSyn), a 140-residue intrinsically disordered protein, comprises the primary proteinaceous component of pathology-associated Lewy body inclusions in Parkinson's disease (PD). Due to its association with PD, αSyn is studied extensively; however, the endogenous structure and physiological roles of this protein are yet to be fully understood. Here, ion mobility-mass spectrometry and native top-down electron capture dissociation fragmentation have been used to elucidate the structural properties associated with a stable, naturally occurring dimeric species of αSyn. This stable dimer appears in both wild-type (WT) αSyn and the PD-associated variant A53E. Furthermore, we integrated a novel method for generating isotopically depleted protein into our native top-down workflow. Isotope depletion increases signal-to-noise ratio and reduces the spectral complexity of fragmentation data, enabling the monoisotopic peak of low abundant fragment ions to be observed. This enables the accurate and confident assignment of fragments unique to the αSyn dimer to be assigned and structural information about this species to be inferred. Using this approach, we were able to identify fragments unique to the dimer, which demonstrates a C-terminal to C-terminal interaction between the monomer subunits. The approach in this study holds promise for further investigation into the structural properties of endogenous multimeric species of αSyn.
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Affiliation(s)
- Kiani Jeacock
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Alexandre Chappard
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Kelly J Gallagher
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - David P A Kilgour
- Chemistry and Forensics, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Mathew H Horrocks
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
| | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, U.K
| | - David J Clarke
- The EastCHEM School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, U.K
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3
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Chikugo A, Irie Y, Tsukano C, Uchino A, Maki T, Kume T, Kawase T, Hirose K, Kageyama Y, Tooyama I, Irie K. Optimization of the Linker Length in the Dimer Model of E22P-Aβ40 Tethered at Position 38. ACS Chem Neurosci 2022; 13:2913-2923. [PMID: 36095282 DOI: 10.1021/acschemneuro.2c00436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Since amyloid β (Aβ) oligomers are more cytotoxic than fibrils, various dimer models have been synthesized. We focused on the C-terminal region that could form a hydrophobic core in the aggregation process and identified a toxic conformer-restricted dimer model (E22P,G38DAP-Aβ40 dimer) with an l,l-2,6-diaminopimelic acid linker (n = 3) at position 38, which exhibited moderate cytotoxicity. We synthesized four additional linkers (n = 2, 4, 5, 7) to determine the most appropriate distance between the two Aβ40 monomers for a toxic dimer model. Each di-Fmoc-protected two-valent amino acid was synthesized from a corresponding dialdehyde or cycloalkene followed by ozonolysis, using a Horner-Wadsworth-Emmons reaction and asymmetric hydrogenation. Then, the corresponding Aβ40 dimer models with these linkers at position 38 were synthesized using the solid-phase Fmoc strategy. Their cytotoxicity toward SH-SY5Y cells suggested that the shorter the linker length, the stronger the cytotoxicity. Particularly, the E22P,G38DAA-Aβ40 dimer (n = 2) formed protofibrillar aggregates and exhibited the highest cytotoxicity, equivalent to E22P-Aβ42, the most cytotoxic analogue of Aβ42. Ion mobility-mass spectrometry (IM-MS) measurement indicated that all dimer models except the E22P,G38DAA-Aβ40 dimer existed as stable oligomers (12-24-mer). NativePAGE analysis supported the IM-MS data, but larger oligomers (30-150-mer) were also detected after a 24 h incubation. Moreover, E22P,G38DAA-Aβ40, E22P,G38DAP-Aβ40, and E22P,G38DAZ-Aβ40 (n = 5) dimers suppressed long-term potentiation (LTP). Overall, the ability to form fibrils with cross β-sheet structures was key to achieving cytotoxicity, and forming stable oligomers less than 150-mer did not correlate with cytotoxicity and LTP suppression.
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Affiliation(s)
- Ayaka Chikugo
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Yumi Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Chihiro Tsukano
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Ayumi Uchino
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Takahito Maki
- Department of Applied Pharmacology, Graduate School of Medical and Pharmaceutical Sciences, University of Toyama, Toyama930-0194, Japan
| | - Toshiaki Kume
- Department of Applied Pharmacology, Graduate School of Medical and Pharmaceutical Sciences, University of Toyama, Toyama930-0194, Japan
| | | | | | - Yusuke Kageyama
- Molecular Neuroscience Research Center, Shiga University of Medical Sciences, Shiga520-2192, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center, Shiga University of Medical Sciences, Shiga520-2192, Japan
| | - Kazuhiro Irie
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
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4
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Lu Y, Salsbury F, Derreumaux P. Impact of A2T and D23N mutations on C99 homodimer conformations. J Chem Phys 2022; 157:085102. [DOI: 10.1063/5.0101622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The proteolytic cleavage of C99 by γ-secretase is the last step in the production of amyloid-β (Aβ) peptides. Previous studies have shown that membrane lipid composition, cholesterol concentration, and mutation in the transmembrane helix modified the structures and fluctuations of C99. In this study, we performed atomistic molecular dynamics simulations of the homodimer of the 55-residue congener of the C-terminal domain of the amyloid protein precursor, C99(1-55), in a POPC-cholesterol lipid bilayer, and we compared the conformational ensemble of WT sequence to those of the A2T and D23N variants. These mutations are particularly interesting as the protective Alzheimer's disease (AD) A2T mutation is known to decrease Aβ production, whereas the early onset AD D23N mutation does not affect Aβ production. We found noticeable differences in the structural ensembles of the three sequences. In particular, A2T varies from both WT and D23N by having long-range effects on the population of the extracellular justamembrane helix, the interface between the G29xxx-G33xxx-G37 motifs and the fluctuations of the transmembrane helical topologies.
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Affiliation(s)
- Yan Lu
- School of Physics, Xidian University, China
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5
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Stanciu GD, Ababei DC, Rusu RN, Bild V, Tamba BI. Exploring the Involvement of the Amyloid Precursor Protein A673T Mutation against Amyloid Pathology and Alzheimer's Disease in Relation to Therapeutic Editing Tools. Pharmaceutics 2022; 14:1270. [PMID: 35745842 PMCID: PMC9228826 DOI: 10.3390/pharmaceutics14061270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Alzheimer's disease (AD) is biologically defined as a complex neurodegenerative condition with a multilayered nature that leads to a progressive decline in cognitive function and irreversible neuronal loss. It is one of the primary diseases among elderly individuals. With an increasing incidence and a high failure rate for pharmaceutical options that are merely symptom-targeting and supportive with many side effects, there is an urgent need for alternative strategies. Despite extensive knowledge on the molecular basis of AD, progress concerning effective disease-modifying therapies has proven to be a challenge. The ability of the CRISPR-Cas9 gene editing system to help identify target molecules or to generate new preclinical disease models could shed light on the pathogenesis of AD and provide promising therapeutic possibilities. Here, we sought to highlight the current understanding of the involvement of the A673T mutation in amyloid pathology, focusing on its roles in protective mechanisms against AD, in relation to the recent status of available therapeutic editing tools.
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Affiliation(s)
- Gabriela Dumitrita Stanciu
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (G.D.S.); (B.-I.T.)
| | - Daniela Carmen Ababei
- Pharmacodynamics and Clinical Pharmacy Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (R.N.R.); (V.B.)
| | - Razvan Nicolae Rusu
- Pharmacodynamics and Clinical Pharmacy Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (R.N.R.); (V.B.)
| | - Veronica Bild
- Pharmacodynamics and Clinical Pharmacy Department, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (R.N.R.); (V.B.)
| | - Bogdan-Ionel Tamba
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania; (G.D.S.); (B.-I.T.)
- Department of Pharmacology, Clinical Pharmacology and Algesiology, Grigore T. Popa University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
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6
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Nguyen TH, Nguyen PH, Ngo ST, Derreumaux P. Effect of Cholesterol Molecules on Aβ1-42 Wild-Type and Mutants Trimers. Molecules 2022; 27:molecules27041395. [PMID: 35209177 PMCID: PMC8879133 DOI: 10.3390/molecules27041395] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Alzheimer’s disease displays aggregates of the amyloid-beta (Aβ) peptide in the brain, and there is increasing evidence that cholesterol may contribute to the pathogenesis of the disease. Though many experimental and theoretical studies have focused on the interactions of Aβ oligomers with membrane models containing cholesterol, an understanding of the effect of free cholesterol on small Aβ42 oligomers is not fully established. To address this question, we report on replica exchange with a solute tempering simulation of an Aβ42 trimer with cholesterol and compare it with a previous replica exchange molecular dynamics simulation. We show that the binding hot spots of cholesterol are rather complex, involving hydrophobic residues L17–F20 and L30–M35 with a non-negligible contribution of loop residues D22–K28 and N-terminus residues. We also examine the effects of cholesterol on the trimers of the disease-causing A21G and disease-protective A2T mutations by molecular dynamics simulations. We show that these two mutations moderately impact cholesterol-binding modes. In our REST2 simulations, we find that cholesterol is rarely inserted into aggregates but rather attached as dimers and trimers at the surface of Aβ42 oligomers. We propose that cholesterol acts as a glue to speed up the formation of larger aggregates; this provides a mechanistic link between cholesterol and Alzheimer’s disease.
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Affiliation(s)
- Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam; (T.H.N.); (S.T.N.)
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam; (T.H.N.); (S.T.N.)
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
- Correspondence:
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7
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Yuan M, Tang X, Han W. Anatomy and Formation Mechanisms of Early Amyloid-β Oligomers with Lateral Branching: Graph Network Analysis on Large-Scale Simulations. Chem Sci 2022; 13:2649-2660. [PMID: 35356670 PMCID: PMC8890322 DOI: 10.1039/d1sc06337e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
Oligomeric amyloid-β aggregates (AβOs) effectively trigger Alzheimer's disease-related toxicity, generating great interest in understanding their structures and formation mechanisms. However, AβOs are heterogeneous and transient, making their structure and formation difficult to study. Here, we performed graph network analysis of tens of microsecond massive simulations of early amyloid-β (Aβ) aggregations at near-atomic resolution to characterize AβO structures with sizes up to 20-mers. We found that AβOs exhibit highly curvilinear, irregular shapes with occasional lateral branches, consistent with recent cryo-electron tomography experiments. We also found that Aβ40 oligomers were more likely to develop branches than Aβ42 oligomers, explaining an experimental observation that only Aβ40 was trapped in network-like aggregates and exhibited slower fibrillization kinetics. Moreover, AβO architecture dissection revealed that their curvilinear appearance is related to the local packing geometries of neighboring peptides and that Aβ40's greater branching ability originates from specific C-terminal interactions at branching interfaces. Finally, we demonstrate that whether Aβ oligomerization causes oligomers to elongate or to branch depends on the sizes and shapes of colliding aggregates. Collectively, this study provides bottom-up structural information for understanding early Aβ aggregation and AβO toxicity. Graph network analysis on large-scale simulations uncovers the differential branching behaviours of large Aβ40 and Aβ42 oligomers.![]()
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Affiliation(s)
- Miao Yuan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Xuan Tang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 China
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8
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Nguyen PH, Tufféry P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol 2022; 2405:95-113. [PMID: 35298810 DOI: 10.1007/978-1-0716-1855-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.
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Affiliation(s)
- Phuong Hoang Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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9
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Das A. Systematic Search for a Predictor for the Clinical Observables of Alzheimer's Disease. J Phys Chem B 2021; 125:12177-12186. [PMID: 34723517 DOI: 10.1021/acs.jpcb.1c06725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
One of the prevailing life-threatening incurable neurodegenerative diseases that are presently endangering human society as a whole, and hence, baffling the entire spectrum of the scientific and pharmaceutical world, is Alzheimer's disease (AD). AD is a manifestation of self-assembly of both wild-type (sporadic) and mutated (familial) forms of the amyloid-β peptide, a proteolytic product of the amyloid precursor protein, where the self-assembly results in the genesis of pathogenic fibrillar aggregates. Currently prevailing diagnostic and hence therapeutic challenges originate from the unavailability of a specific predictor for clinical observables. The continuous emergence of novel pathogenic mutants with unpredictable phenotypes adds immensely to the nonspecific nature of the problem. The current research reports a simple physical parameter, the binding affinity of a protofilament to its protofibril, which predicts the clinical observables of familial AD with astounding accuracy and more importantly, without any adjustable parameters.
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Affiliation(s)
- Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411 008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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10
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Kennedy-Britten OD, Alshammari N, Platts JA. Accelerated Molecular Dynamics to Explore the Binding of Transition Metals to Amyloid-β. ACS Chem Neurosci 2021; 12:4065-4075. [PMID: 34669379 DOI: 10.1021/acschemneuro.1c00466] [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] [Indexed: 01/12/2023] Open
Abstract
We report the accelerated molecular dynamics (aMD) simulation of amyloid-β (Aβ) peptides of four different lengths (16, 28, 40, and 42 residues) and their complexes when bound to Cu(II), Fe(II), or Zn(II). 600 ns equilibrated trajectory data were analyzed for each structure from three independent 200 ns aMD simulations, generating 16 aMD trajectories. We show that the presence of a metal ion leads to reduced size and decreased mobility relative to the free peptide due to the anchoring effect of the ions. The reduced mobility was shown largely to be due to the restricted movement in N-terminal residues, most notably Asp1 and His6 that are involved in the metal-ion coordination in all cases. Significant disruption of the secondary structure and patterns of salt bridge interactions arise on the coordination of metal ions. In this regard, similarities were noted between results for Zn(II) and Fe(II), whereas results for Cu(II) are more comparable to that of the free peptides. Reweighting of free energy surfaces was carried out from aMD data to identify the properties and descriptions of local minima structures.
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Affiliation(s)
| | - Nadiyah Alshammari
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - James A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
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11
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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.
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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
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12
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Michno W, Blennow K, Zetterberg H, Brinkmalm G. Refining the amyloid β peptide and oligomer fingerprint ambiguities in Alzheimer's disease: Mass spectrometric molecular characterization in brain, cerebrospinal fluid, blood, and plasma. J Neurochem 2021; 159:234-257. [PMID: 34245565 DOI: 10.1111/jnc.15466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 01/05/2023]
Abstract
Since its discovery, amyloid-β (Aβ) has been the principal target of investigation of in Alzheimer's disease (AD). Over the years however, no clear correlation was found between the Aβ plaque burden and location, and AD-associated neurodegeneration and cognitive decline. Instead, diagnostic potential of specific Aβ peptides and/or their ratio, was established. For instance, a selective reduction in the concentration of the aggregation-prone 42 amino acid-long Aβ peptide (Aβ42) in cerebrospinal fluid (CSF) was put forward as reflective of Aβ peptide aggregation in the brain. With time, Aβ oligomers-the proposed toxic Aβ intermediates-have emerged as potential drivers of synaptic dysfunction and neurodegeneration in the disease process. Oligomers are commonly agreed upon to come in different shapes and sizes, and are very poorly characterized when it comes to their composition and their "toxic" properties. The concept of structural polymorphism-a diversity in conformational organization of amyloid aggregates-that depends on the Aβ peptide backbone, makes the characterization of Aβ aggregates and their role in AD progression challenging. In this review, we revisit the history of Aβ discovery and initial characterization and highlight the crucial role mass spectrometry (MS) has played in this process. We critically review the common knowledge gaps in the molecular identity of the Aβ peptide, and how MS is aiding the characterization of higher order Aβ assemblies. Finally, we go on to present recent advances in MS approaches for characterization of Aβ as single peptides and oligomers, and convey our optimism, as to how MS holds a promise for paving the way for progress toward a more comprehensive understanding of Aβ in AD research.
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Affiliation(s)
- Wojciech Michno
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.,Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Kaj Blennow
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK.,UK Dementia Research Institute at UCL, London, UK
| | - Gunnar Brinkmalm
- Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
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13
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Sun Y, Kakinen A, Wan X, Moriarty N, Hunt CP, Li Y, Andrikopoulos N, Nandakumar A, Davis TP, Parish CL, Song Y, Ke PC, Ding F. Spontaneous Formation of β-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta. NANO TODAY 2021; 38:101125. [PMID: 33936250 PMCID: PMC8081394 DOI: 10.1016/j.nantod.2021.101125] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Soluble low-molecular-weight oligomers formed during the early aggregation of amyloid peptides have been hypothesized as a major toxic species of amyloidogenesis. Herein, we performed the first synergic in silico, in vitro and in vivo validations of the structure, dynamics and toxicity of Aβ42 oligomers. Aβ peptides readily assembled into β-rich oligomers comprised of extended β-hairpins and β-strands. Nanosized β-barrels were observed with certainty with simulations, transmission electron microscopy and Fourier transform infrared spectroscopy, corroborated by immunohistochemistry, cell viability, apoptosis, inflammation, autophagy and animal behavior assays. Secondary and tertiary structural proprieties of these oligomers, such as the sequence regions with high β-sheet propensities and inter-residue contact frequency patterns, were similar to the properties known for Aβ fibrils. The unambiguous spontaneous formation of β-barrels in the early aggregation of Aβ42 supports their roles as the common toxic intermediates in Alzheimer's pathobiology and a target for Alzheimer's therapeutics.
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Affiliation(s)
- Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Xulin Wan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Food Science, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
| | - Niamh Moriarty
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Cameron P.J. Hunt
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Yuhuan Li
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas P. Davis
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Clare L. Parish
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Yang Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Pu Chun Ke
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
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Limegrover CS, LeVine H, Izzo NJ, Yurko R, Mozzoni K, Rehak C, Sadlek K, Safferstein H, Catalano SM. Alzheimer's protection effect of A673T mutation may be driven by lower Aβ oligomer binding affinity. J Neurochem 2021; 157:1316-1330. [PMID: 33025581 PMCID: PMC8246829 DOI: 10.1111/jnc.15212] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/16/2022]
Abstract
Several mutations conferring protection against Alzheimer's disease (AD) have been described, none as profound as the A673T mutation, where carriers are four times less likely to get AD compared to noncarriers. This mutation results in reduced amyloid beta (Aβ) protein production in vitro and lower lifetime Aβ concentration in carriers. Better understanding of the protective mechanisms of the mutation may provide important insights into AD pathophysiology and identify productive therapeutic intervention strategies for disease modification. Aβ(1-42) protein forms oligomers that bind saturably to a single receptor site on neuronal synapses, initiating the downstream toxicities observed in AD. Decreased formation, toxicity, or stability of soluble Aβ oligomers, or reduction of synaptic binding of these oligomers, may combine with overall lower Aβ concentration to underlie A673T's disease protecting mechanism. To investigate these possibilities, we compared the formation rate of soluble oligomers made from Icelandic A673T mutant and wild type (wt) Aβ(1-42) synthetic protein, the amount and intensity of oligomer bound to mature primary rat hippocampal/cortical neuronal synapses, and the potency of bound oligomers to impact trafficking rate in neurons in vitro using a physiologically relevant oligomer preparation method. At equal protein concentrations, mutant protein forms approximately 50% or fewer oligomers of high molecular weight (>50 kDa) compared to wt protein. Mutant oligomers are twice as potent at altering the cellular vesicle trafficking rate as wt at equivalent concentrations, however, mutant oligomers have a >4-fold lower binding affinity to synaptic receptors (Kd = 1,950 vs. 442 nM). The net effect of these differences is a lower overall toxicity at a given concentration. This study demonstrates for the first time that mutant A673T Aβ oligomers prepared with this method have fundamentally different assembly characteristics and biological impact from wt protein and indicates that its disease protecting mechanism may result primarily from the mutant protein's much lower binding affinity to synaptic receptors. This suggests that therapeutics that effectively reduce oligomer binding to synapses in the brain may be beneficial in AD.
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Affiliation(s)
| | - Harry LeVine
- Sanders‐Brown Center on AgingUniversity of KentuckyLexingtonKYUSA
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15
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Li X, Lao Z, Zou Y, Dong X, Li L, Wei G. Mechanistic Insights into the Co-Aggregation of Aβ and hIAPP: An All-Atom Molecular Dynamic Study. J Phys Chem B 2021; 125:2050-2060. [PMID: 33616398 DOI: 10.1021/acs.jpcb.0c11132] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Patients with Alzheimer's disease (AD) have a high risk of developing Type II diabetes (T2D). The co-aggregation of the two disease-related proteins, Aβ and hIAPP, has been proposed as a potential molecular mechanism. However, the detailed Aβ-hIAPP interactions and structural characteristics of co-aggregates are mostly unknown at atomic level. Here, we explore the conformational ensembles of the Aβ-hIAPP heterodimer and Aβ or hIAPP homodimer by performing all-atom explicit-solvent replica exchange molecular dynamic simulations. Our simulations show that the interaction propensity of Aβ-hIAPP in the heterodimer is comparable with that of Aβ-Aβ/hIAPP-hIAPP in the homodimer. Similar hot spot residues of Aβ/hIAPP in the homodimer and heterodimer are identified, indicating that both Aβ and hIAPP have similar molecular recognition sites for self-aggregation and co-aggregation. Aβ in the heterodimer possesses three high β-sheet probability regions: the N-terminal region E3-H6, the central hydrophobic core region K16-E22, and the C-terminal hydrophobic region I31-A41, which is highly similar to Aβ in the homodimer. More importantly, in the heterodimer, the regions E3-H6, F19-E22, and I31-M35 of Aβ and the amyloid core region N20-T30 of hIAPP display higher β-sheet probability than they do in homodimer, implying their crucial roles in the formation of β-sheet-rich co-aggregates. Our study sheds light on the co-aggregation of Aβ and hIAPP at an atomic level, which will be helpful for an in-depth understanding of the molecular mechanism for epidemiological correlation of AD and T2D.
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Affiliation(s)
- Xuhua Li
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China.,MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zenghui Lao
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Yu Zou
- Department of Sport and Exercise Science, College of Education, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310007 Zhejiang, China
| | - Xuewei Dong
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Le Li
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
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16
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Park KW, Wood CA, Li J, Taylor BC, Oh S, Young NL, Jankowsky JL. Gene therapy using Aβ variants for amyloid reduction. Mol Ther 2021; 29:2294-2307. [PMID: 33647457 DOI: 10.1016/j.ymthe.2021.02.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/30/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Numerous aggregation inhibitors have been developed with the goal of blocking or reversing toxic amyloid formation in vivo. Previous studies have used short peptide inhibitors targeting different amyloid β (Aβ) amyloidogenic regions to prevent aggregation. Despite the specificity that can be achieved by peptide inhibitors, translation of these strategies has been thwarted by two key obstacles: rapid proteolytic degradation in the bloodstream and poor transfer across the blood-brain barrier. To circumvent these problems, we have created a minigene to express full-length Aβ variants in the mouse brain. We identify two variants, F20P and F19D/L34P, that display four key properties required for therapeutic use: neither peptide aggregates on its own, both inhibit aggregation of wild-type Aβ in vitro, promote disassembly of pre-formed fibrils, and diminish toxicity of Aβ oligomers. We used intraventricular injection of adeno-associated virus (AAV) to express each variant in APP/PS1 transgenic mice. Lifelong expression of F20P, but not F19D/L34P, diminished Aβ levels, plaque burden, and plaque-associated neuroinflammation. Our findings suggest that AAV delivery of Aβ variants may offer a novel therapeutic strategy for Alzheimer's disease. More broadly our work offers a framework for identifying and delivering peptide inhibitors tailored to other protein-misfolding diseases.
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Affiliation(s)
- Kyung-Won Park
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Caleb A Wood
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bethany C Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - SaeWoong Oh
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon City, 16419 GyunggiDo, Republic of Korea
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joanna L Jankowsky
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Neurology, and Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
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17
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Man VH, Wang J, Derreumaux P, Nguyen PH. Nonequilibrium molecular dynamics simulations of infrared laser-induced dissociation of a tetrameric Aβ42 β-barrel in a neuronal membrane model. Chem Phys Lipids 2020; 234:105030. [PMID: 33347835 DOI: 10.1016/j.chemphyslip.2020.105030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 11/29/2022]
Abstract
Experimental studies have reported that the amyloid-β proteins can form pores in cell membranes, and this could be one possible source of toxicity in Alzheimer's disease. Dissociation of these pores could therefore be a potential therapeutic approach. It is known that high photon density free-electron laser experiments and laser-induced nonequilibrium molecular dynamics simulations (NEMD) can dissociate amyloid fibrils at specific frequencies in vitro. Our question is whether NEMD simulations can dissociate amyloid pores in a bilayer mimicking a neuronal membrane, and as an example, we select a tetrameric Aβ42 β-barrel. Our simulations shows that the resonance between the laser field and the amide I vibrational mode of the barrel destabilises all intramolecular and intermolecular hydrogen bonds of Aβ42 and converts the β-barrel to a random/coil disordered oligomer. Starting from this disordered oligomer, extensive standard MD simulations shows sampling of disordered Aβ42 states without any increase of β-sheet and reports that the orientational order of lipids is minimally disturbed. Interestingly, the frequency to be employed to dissociate this beta-barrel is specific to the amino acid sequence. Taken together with our previous simulation results, this study indicates that infrared laser irradiation can dissociate amyloid fibrils and oligomers in bulk solution and in a membrane environment without affecting the surrounding molecules, offering therefore a promising way to retard the progression of AD.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh, Vietnam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh, Vietnam.
| | - Phuong H Nguyen
- CNRS, Université de Paris, UPR9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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18
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Li H, Salimi A, Lee JY. Intrinsic Origin of Amyloid Aggregation: Collective Effects of the Mutation and Tautomerism of Histidine. ACS Chem Neurosci 2019; 10:4729-4734. [PMID: 31600048 DOI: 10.1021/acschemneuro.9b00491] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mutation is considered an important factor in the accumulation of amyloid-β (Aβ), which is a hallmark of Alzheimer's disease (AD). A2V Aβ40 shows a higher aggregation tendency; however, the existing knowledge is not sufficient to explain the mechanism. We performed replica-exchange molecular dynamics simulations (REMD) to investigate the structural properties of A2V Aβ40 monomers and consider the tautomerism of histidine. The collective effects of the mutation and tautomerism leads A2V Aβ40 to much higher β-sheet and lower α-helix contents than WT Aβ40, which may explain the enhanced aggregation kinetics of A2V Aβ40 with respect to WT Aβ40. The current research provides new insights on understanding the pathology of AD.
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Affiliation(s)
- Hao Li
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
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19
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Man VH, He X, Ji B, Liu S, Xie XQ, Wang J. Molecular Mechanism and Kinetics of Amyloid-β 42 Aggregate Formation: A Simulation Study. ACS Chem Neurosci 2019; 10:4643-4658. [PMID: 31660732 DOI: 10.1021/acschemneuro.9b00473] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
As an important neuropathological hallmark of Alzheimer's disease (AD), the oligomerization of amyloid-β (Aβ) peptides has been intensively investigated in both theoretical and experimental studies. However, the oligomerization space in terms of the kinetics, molecular mechanism, and oligomer structures remains mysterious to us. An equation that can quantitatively describe the time it takes for Aβ oligomers to appear in the human brain at a given Aβ monomer concentration is extremely vital for us to understand the development and disease progression of AD. In this study, we utilized molecular dynamics (MD) simulations to investigate the oligomerization of Aβ42 peptides at five different monomer concentrations. We have elucidated the formation pathways of Aβ tetramers, characterized the oligomer structures, estimated the oligomerization time for Aβ dimers, trimers, and tetramers, and for the first-time derived equations that could quantitatively describe the relationship between the oligomerization time and the monomer concentration. Applying these equations, our prediction of oligomerization time agrees well with the experimental and clinical findings, in spite of the limitations of our oligomerization simulations. We have found that the Aβ oligomerization time depends on the monomer concentration by a power of -2.4. The newly established equations will enable us to quantitatively estimate the risk score of AD, which is a function of age. Moreover, we have identified the most dominant pathway of forming Aβ tetramers, probably the most important and toxic Aβ oligomer. Our results have shown that the structures of Aβ42 dimer, trimer, and tetramer, which are distinguishable from each other, depend on the monomer concentration at which the oligomers form. Representative oligomer structures, which can serve as potential drug targets, have been identified by clustering analysis. The MD sampling adequacy has been validated by the excellent agreement between the calculated and measured collisional cross section (CCS) parameters (the prediction errors are within 2%). In a conclusion, this study provides the kinetics and structure basis for developing inhibitors to decelerate the Aβ oligomerization process.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Beihong Ji
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Shuhan Liu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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20
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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
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21
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Nguyen PH, Campanera JM, Ngo ST, Loquet A, Derreumaux P. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution. J Phys Chem B 2019; 123:6750-6756. [DOI: 10.1021/acs.jpcb.9b05288] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Phuong H. Nguyen
- CNRS, Université de Paris, UPR 9080,
Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Josep M. Campanera
- Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nanoobjects, UMR5248 CNRS, Université de Bordeaux, Bordeaux, France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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22
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Castro MA, Hadziselimovic A, Sanders CR. The vexing complexity of the amyloidogenic pathway. Protein Sci 2019; 28:1177-1193. [PMID: 30897251 PMCID: PMC6566549 DOI: 10.1002/pro.3606] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
Abstract
The role of the amyloidogenic pathway in the etiology of Alzheimer's disease (AD), particularly the common sporadic late onset forms of the disease, is controversial. To some degree, this is a consequence of the failure of drug and therapeutic antibody trials based either on targeting the proteases in this pathway or its amyloid end products. Here, we explore the formidable complexity of the biochemistry and cell biology associated with this pathway. For example, we review evidence that the immediate precursor of amyloid-β, the C99 domain of the amyloid precursor protein (APP), may itself be toxic. We also review important new results that appear to finally establish a direct genetic link between mutations in APP and the sporadic forms of AD. Based on the complexity of amyloidogenesis, it seems possible that a major contributor to the failure of related drug trials is that we have an incomplete understanding of this pathway and how it is linked to Alzheimer's pathogenesis. If so, this highlights a need for further characterization of this pathway, not its abandonment.
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Affiliation(s)
- Manuel A. Castro
- Departments of Biochemistry and MedicineVanderbilt University School of MedicineNashvilleTennessee 37240
| | - Arina Hadziselimovic
- Departments of Biochemistry and MedicineVanderbilt University School of MedicineNashvilleTennessee 37240
| | - Charles R. Sanders
- Departments of Biochemistry and MedicineVanderbilt University School of MedicineNashvilleTennessee 37240
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23
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Ngo ST, Derreumaux P, Vu VV. Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca2+ Ions. J Phys Chem B 2019; 123:2645-2653. [DOI: 10.1021/acs.jpcb.8b10792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris, 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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24
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Okada Y, Okubo K, Ikeda K, Yano Y, Hoshino M, Hayashi Y, Kiso Y, Itoh-Watanabe H, Naito A, Matsuzaki K. Toxic Amyloid Tape: A Novel Mixed Antiparallel/Parallel β-Sheet Structure Formed by Amyloid β-Protein on GM1 Clusters. ACS Chem Neurosci 2019; 10:563-572. [PMID: 30346704 DOI: 10.1021/acschemneuro.8b00424] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The abnormal aggregation of amyloid β-protein (Aβ) is considered central in the pathogenesis of Alzheimer's disease. We focused on membrane-mediated amyloidogenesis and found that amyloid fibrils formed on monosialoganglioside GM1 clusters were more toxic than those formed in aqueous solution. In this study, we investigated the structure of the toxic fibrils by Aβ-(1-40) in detail in comparison with less-toxic fibrils formed in aqueous solution. The less-toxic fibrils contain in-resister parallel β-sheets, whereas the structure of the toxic fibrils is unknown. Atomic force microscopy revealed that the toxic fibrils had a flat, tape-like morphology composed of a single β-sheet layer. Isotope-edited infrared spectroscopy indicated that almost the entire sequence of Aβ is included in the β-sheet. Chemical cross-linking experiments using Cys-substituted Aβs suggested that the fibrils mainly contained both in-resister parallel and two-residue-shifted antiparallel β-sheet structures. Solid-state NMR experiments also supported this conclusion. Thus, the toxic fibrils were found to possess a novel unique structure.
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Affiliation(s)
- Yuki Okada
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kaori Okubo
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Keisuke Ikeda
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshio Hayashi
- Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Yoshiaki Kiso
- Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
- Laboratory of Peptide Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Hikari Itoh-Watanabe
- Graduate School of Engineering, Yokohama Naitional University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama Naitional University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
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25
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Jin Y, Sun Y, Chen Y, Lei J, Wei G. Molecular dynamics simulations reveal the mechanism of graphene oxide nanosheet inhibition of Aβ1–42 peptide aggregation. Phys Chem Chem Phys 2019; 21:10981-10991. [DOI: 10.1039/c9cp01803d] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Graphene oxide nanosheets inhibit Aβ1–42 aggregation by weakening inter-peptide interactions and reducing β-sheet contents mostly via salt bridge, hydrogen bonding and cation–π interactions with charged residues.
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Affiliation(s)
- Yibo Jin
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Fudan University
- Shanghai 200433
| | - Yunxiang Sun
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Fudan University
- Shanghai 200433
| | - Yujie Chen
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Fudan University
- Shanghai 200433
| | - Jiangtao Lei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Fudan University
- Shanghai 200433
| | - Guanghong Wei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Fudan University
- Shanghai 200433
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26
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Atrián-Blasco E, Gonzalez P, Santoro A, Alies B, Faller P, Hureau C. Cu and Zn coordination to amyloid peptides: From fascinating chemistry to debated pathological relevance. Coord Chem Rev 2018; 375:38-55. [PMID: 30262932 DOI: 10.1016/j.ccr.2018.04.007] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Several diseases share misfolding of different peptides and proteins as a key feature for their development. This is the case of important neurodegenerative diseases such as Alzheimer's and Parkinson's diseases and type II diabetes mellitus. Even more, metal ions such as copper and zinc might play an important role upon interaction with amyloidogenic peptides and proteins, which could impact their aggregation and toxicity abilities. In this review, the different coordination modes proposed for copper and zinc with amyloid-β, α-synuclein and IAPP will be reviewed as well as their impact on the aggregation, and ROS production in the case of copper. In addition, a special focus will be given to the mutations that affect metal binding and lead to familial cases of the diseases. Different modifications of the peptides that have been observed in vivo and could be relevant for the coordination of metal ions are also described.
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Affiliation(s)
- Elena Atrián-Blasco
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099 31077 Toulouse Cedex 4, France
- University of Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France
| | - Paulina Gonzalez
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| | - Alice Santoro
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| | - Bruno Alies
- Université de Bordeaux, ChemBioPharm INSERM U1212 CNRS UMR 5320, Bordeaux, France
| | - Peter Faller
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| | - Christelle Hureau
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099 31077 Toulouse Cedex 4, France
- University of Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France
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27
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Nguyen PH, del Castillo-Frias MP, Berthoumieux O, Faller P, Doig AJ, Derreumaux P. Amyloid-β/Drug Interactions from Computer Simulations and Cell-Based Assays. J Alzheimers Dis 2018; 64:S659-S672. [DOI: 10.3233/jad-179902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | - Maria P. del Castillo-Frias
- Manchester Institute of Biotechnology and Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Olivia Berthoumieux
- CNRS, LCC (Laboratoire de Chimie de Coordination), Toulouse Cedex 4, France et Université de Toulouse, UPS, INPT, Toulouse Cedex 4, France
| | - Peter Faller
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, Strasbourg, France
| | - Andrew J. Doig
- Manchester Institute of Biotechnology and Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
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28
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Ngo ST, Hung HM, Hong ND, Tung NT. The influences of E22Q mutant on solvated 3Aβ 11-40 peptide: A REMD study. J Mol Graph Model 2018; 83:122-128. [PMID: 29902674 DOI: 10.1016/j.jmgm.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/03/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
The residue E22 plays a critical role in the aggregation process of Amyloid beta (Aβ) peptides. The effect of E22Q mutant on the shapes of the solvated Aβ11-40 trimer is clarified using a replica exchange molecular dynamics (REMD) simulation employing ∼20.6 μs of MD simulations with 48 disparate replicas. The increase of intramolecular polar contacts and salt bridge between the residue D23 to residues (24-29) was observed. The residual secondary structure of the mutated trimer is shifted in a similar way to the picture observed in previous investigations of F19W mutant. The free energy surface (FES) of the mutated E22Q system has a fewer number of minima in comparison with the wild-type trimer. The optimized shapes of the mutated E22Q form a significant increase in beta structure (47%) and serious decrease in coil content (46%) compared with the wild-type (of 36 and 56%, respectively). The binding affinity of constituting chains to the rest is of -43.7 ± 6.5 kcal/mol, implying that the representative structure of E22Q is more stable than the wild-type one. Furthermore, the E22Q mutant increases the size of stable structures due to larger collision cross section (CCS) and solvent accessible area (SASA). The observed results may enhance the Aβ inhibition throughout the contribution to the knowledge of the Aβ oligomerization/aggregation.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Nam Dao Hong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science and Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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29
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Zhang L, Trushin S, Christensen TA, Tripathi U, Hong C, Geroux RE, Howell KG, Poduslo JF, Trushina E. Differential effect of amyloid beta peptides on mitochondrial axonal trafficking depends on their state of aggregation and binding to the plasma membrane. Neurobiol Dis 2018; 114:1-16. [PMID: 29477640 PMCID: PMC5926207 DOI: 10.1016/j.nbd.2018.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/03/2018] [Accepted: 02/07/2018] [Indexed: 12/20/2022] Open
Abstract
Inhibition of mitochondrial axonal trafficking by amyloid beta (Aβ) peptides has been implicated in early pathophysiology of Alzheimer's Disease (AD). Yet, it remains unclear whether the loss of motility inevitably induces the loss of mitochondrial function, and whether restoration of axonal trafficking represents a valid therapeutic target. Moreover, while some investigations identify Aβ oligomers as the culprit of trafficking inhibition, others propose that fibrils play the detrimental role. We have examined the effect of a panel of Aβ peptides with different mutations found in familial AD on mitochondrial motility in primary cortical mouse neurons. Peptides with higher propensity to aggregate inhibit mitochondrial trafficking to a greater extent with fibrils inducing the strongest inhibition. Binding of Aβ peptides to the plasma membrane was sufficient to induce trafficking inhibition where peptides with reduced plasma membrane binding and internalization had lesser effect on mitochondrial motility. We also found that Aβ peptide with Icelandic mutation A673T affects axonal trafficking of mitochondria but has very low rates of plasma membrane binding and internalization in neurons, which could explain its relatively low toxicity. Inhibition of mitochondrial dynamics caused by Aβ peptides or fibrils did not instantly affect mitochondrial bioenergetic and function. Our results support a mechanism where inhibition of axonal trafficking is initiated at the plasma membrane by soluble low molecular weight Aβ species and is exacerbated by fibrils. Since trafficking inhibition does not coincide with the loss of mitochondrial function, restoration of axonal transport could be beneficial at early stages of AD progression. However, strategies designed to block Aβ aggregation or fibril formation alone without ensuring the efficient clearance of soluble Aβ may not be sufficient to alleviate the trafficking phenotype.
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Affiliation(s)
- Liang Zhang
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.
| | - Sergey Trushin
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.
| | - Trace A Christensen
- Microscopy and Cell Analysis Core Facility, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA.
| | - Utkarsh Tripathi
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.
| | - Courtney Hong
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Rachel E Geroux
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.
| | - Kyle G Howell
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA; Microscopy and Cell Analysis Core Facility, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA.
| | - Joseph F Poduslo
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.
| | - Eugenia Trushina
- Department of Neurology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.
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30
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Das P, Matysiak S, Mittal J. Looking at the Disordered Proteins through the Computational Microscope. ACS CENTRAL SCIENCE 2018; 4:534-542. [PMID: 29805999 PMCID: PMC5968442 DOI: 10.1021/acscentsci.7b00626] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 05/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) have attracted wide interest over the past decade due to their surprising prevalence in the proteome and versatile roles in cell physiology and pathology. A large selection of IDPs has been identified as potential targets for therapeutic intervention. Characterizing the structure-function relationship of disordered proteins is therefore an essential but daunting task, as these proteins can adapt transient structure, necessitating a new paradigm for connecting structural disorder to function. Molecular simulation has emerged as a natural complement to experiments for atomic-level characterizations and mechanistic investigations of this intriguing class of proteins. The diverse range of length and time scales involved in IDP function requires performing simulations at multiple levels of resolution. In this Outlook, we focus on summarizing available simulation methods, along with a few interesting example applications. We also provide an outlook on how these simulation methods can be further improved in order to provide a more accurate description of IDP structure, binding, and assembly.
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Affiliation(s)
- Payel Das
- IBM Thomas J.
Watson Research Center, Yorktown Heights, New York 10598, United States
- E-mail:
| | - Silvina Matysiak
- Fischell
Department of Bioengineering, University
of Maryland, College Park, Maryland 20742, United States
| | - Jeetain Mittal
- Department
of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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31
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Foroutanpay B, Kumar J, Kang S, Danaei N, Westaway D, Sim V, Kar S. The Effects of N-terminal Mutations on β-amyloid Peptide Aggregation and Toxicity. Neuroscience 2018; 379:177-188. [DOI: 10.1016/j.neuroscience.2018.03.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 03/01/2018] [Accepted: 03/12/2018] [Indexed: 12/31/2022]
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32
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Jin Y, Sun Y, Lei J, Wei G. Dihydrochalcone molecules destabilize Alzheimer's amyloid-β protofibrils through binding to the protofibril cavity. Phys Chem Chem Phys 2018; 20:17208-17217. [DOI: 10.1039/c8cp01631c] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dihydrochalcone molecules destabilize Aβ17–42protofibrils by disrupting the N-terminal β1 region and the turn region through binding to the protofibril cavity.
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Affiliation(s)
- Yibo Jin
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Yunxiang Sun
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Jiangtao Lei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
| | - Guanghong Wei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Collaborative Innovation Center of Advanced Microstructures (Nanjing)
- Fudan University
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33
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Barz B, Liao Q, Strodel B. Pathways of Amyloid-β Aggregation Depend on Oligomer Shape. J Am Chem Soc 2017; 140:319-327. [PMID: 29235346 DOI: 10.1021/jacs.7b10343] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
One of the main research topics related to Alzheimer's disease is the aggregation of the amyloid-β peptide, which was shown to follow different pathways for the two major alloforms of the peptide, Aβ40 and the more toxic Aβ42. Experimental studies emphasized that oligomers of specific sizes appear in the early aggregation process in different quantities and might be the key toxic agents for each of the two alloforms. We use transition networks derived from all-atom molecular dynamics simulations to show that the oligomers leading to the type of oligomer distributions observed in experiments originate from compact conformations. Extended oligomers, on the other hand, contribute more to the production of larger aggregates thus driving the aggregation process. We further demonstrate that differences in the aggregation pathways of the two Aβ alloforms occur as early as during the dimer stage. The higher solvent-exposure of hydrophobic residues in Aβ42 oligomers contributes to the different aggregation pathways of both alloforms and also to the increased cytotoxicity of Aβ42.
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Affiliation(s)
- Bogdan Barz
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH , 52425 Jülich, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , 40225 Düsseldorf, Germany
| | - Qinghua Liao
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH , 52425 Jülich, Germany.,Department of Cell and Molecular Biology, Uppsala University , S-75124 Uppsala, Sweden
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH , 52425 Jülich, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , 40225 Düsseldorf, Germany
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34
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Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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35
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36
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Weber OC, Uversky VN. How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β 42 in water. INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1377813. [PMID: 30250773 DOI: 10.1080/21690707.2017.1377813] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022]
Abstract
Amyloid-β42 (Aβ42) is an intrinsically disordered peptide intimately related to the pathogenesis of several neurodegenerative diseases. Molecular dynamics (MD) simulations are extensively utilized in the characterization of the structures and conformational dynamics of intrinsically disordered proteins (IDPs) including Aβ42, with AMBER and CHARMM parameters being commonly used in these studies. Recently, comparison of the effects of force field parameters on the Aβ42 structures has started to gain significant attention. In this study, the structures of Aβ42 are simulated using AMBER FF99SB and CHARMM22/CMAP parameters via replica exchange MD simulations utilizing a widely used clustering algorithm. These analyses show that the structural properties (extent and positioning of the elements of secondary and tertiary structure), radius of gyration values, number and position of salt bridges are extremely dependent on the chosen force field parameters notably with the usage of clustering algorithms. For example, predicted secondary structure elements, which are of the great importance for better understanding of the molecular mechanisms of neurodegenerative diseases, deviate enormously in models generated using currently available force field parameters for proteins. Based on the derived models, chemical shift values are calculated and compared to the experimentally determined data. This comparison revealed that although both force field parameters yield results in agreement with experiments, the obtained structural properties were rather different using a clustering algorithm. In other words, these results show that the predicted structures depend heavily on the force field parameters. Importantly, since none of the force field parameters currently utilized in MD studies were developed specifically taking into account the disordered nature of IDPs, these findings clearly indicate that new force field parameters have to be developed for IDPs considering their rapid flexibility and dynamics with high amplitude. Furthermore, molecular simulations of IDPs are typically conducted using one water volume. We show that the confined aqueous volume impacts the predicted structural properties of Aβ42 in water. Although up to date, confined aqueous volume effects have been ignored in the MD simulations of IDPs in water, our data indicate that these effects have to be taken into account in predicting the structural and thermodynamic properties of disordered proteins in solution.
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Affiliation(s)
- Orkid Coskuner Weber
- Department of Chemistry and Neurosciences Institute, The University of Texas at San Antonio, San Antonio, TX, USA.,Institut für Physikalische Chemie, Universität zu Köln, Köln, Germany.,Molecular Biotechnology Division, Turkisch-Deutsche Universität, Istanbul Turkey
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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37
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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.
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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:
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38
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Chakraborty S, Das P. Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors. Sci Rep 2017; 7:9941. [PMID: 28855598 PMCID: PMC5577341 DOI: 10.1038/s41598-017-10212-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/04/2017] [Indexed: 02/01/2023] Open
Abstract
Alzheimer’s disease (AD) is characterized by deposition of amyloid beta (Aβ) peptides into senile plaques in the brain. While most familial mutations are associated with early-onset AD, recent studies report the AD-protective nature of two genetic human Aβ variants, i.e. A2T and A2V, in the heterozygous state. The mixture of A2V Aβ1-6 (Aβ6) hexapeptide and WT Aβ1–42 (Αβ42) is also found neuroprotective. Motivated by these findings, in this study we investigate the effects of WT, A2V, and A2T Aβ6 hexapeptide binding on the monomeric WT Aβ42 landscape. For this purpose, we have performed extensive atomistic Replica Exchange Molecular Dynamics simulations, elucidating preferential binding of Aβ42 with the A2V and A2T hexapeptides compared to WT Aβ6. A notable reorganization of the Aβ42 landscape is revealed due to hexapeptide association, as manifested by lowering of transient interactions between the central and C-terminal hydrophobic patches. Concurrently, Aβ6-bound Aβ42 monomer exhibits alternative structural features that are strongly dependent on the hexapeptide sequence. For example, a central helix is more frequently populated within the A2T-bound monomer, while A2V-bound Aβ42 is often enhanced in overall disorder. Taken together, the present simulations offer novel molecular insights onto the effect of the N-terminal hexapeptide binding on the Aβ42 monomer structure, which might help in explaining their reported amyloid inhibition properties.
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Affiliation(s)
| | - Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA.
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39
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Bleiholder C, Bowers MT. The Solution Assembly of Biological Molecules Using Ion Mobility Methods: From Amino Acids to Amyloid β-Protein. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:365-386. [PMID: 28375705 PMCID: PMC6287953 DOI: 10.1146/annurev-anchem-071114-040304] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) methods are increasingly used to study noncovalent assemblies of peptides and proteins. This review focuses on the noncovalent self-assembly of amino acids and peptides, systems at the heart of the amyloid process that play a central role in a number of devastating diseases. Three different systems are discussed in detail: the 42-residue peptide amyloid-β42 implicated in the etiology of Alzheimer's disease, several amyloid-forming peptides with 6-11 residues, and the assembly of individual amino acids. We also discuss from a more fundamental perspective the processes that determine how quickly proteins and their assemblies denature when the analyte ion has been stripped of its solvent in an IMS-MS measurement and how to soften the measurement so that biologically meaningful data can be recorded.
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Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306;
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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40
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Wolff M, Zhang-Haagen B, Decker C, Barz B, Schneider M, Biehl R, Radulescu A, Strodel B, Willbold D, Nagel-Steger L. Aβ42 pentamers/hexamers are the smallest detectable oligomers in solution. Sci Rep 2017; 7:2493. [PMID: 28559586 PMCID: PMC5449387 DOI: 10.1038/s41598-017-02370-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/11/2017] [Indexed: 12/14/2022] Open
Abstract
Amyloid β (Aβ) oligomers may play a decisive role in Alzheimer's disease related neurodegeneration, but their structural properties are poorly understood. In this report, sedimentation velocity centrifugation, small angle neutron scattering (SANS) and molecular modelling were used to identify the small oligomeric species formed by the 42 amino acid residue long isoform of Aβ (Aβ42) in solution, characterized by a sedimentation coefficient of 2.56 S, and a radius of gyration between 2 and 4 nm. The measured sedimentation coefficient is in close agreement with the sedimentation coefficient calculated for Aβ42 hexamers using MD simulations at µM concentration. To the best of our knowledge this is the first report detailing the Aβ42 oligomeric species by SANS measurements. Our results demonstrate that the smallest detectable species in solution are penta- to hexamers. No evidences for the presence of dimers, trimers or tetramers were found, although the existence of those Aβ42 oligomers at measurable quantities had been reported frequently.
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Affiliation(s)
- Martin Wolff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biochemie, University Potsdam, 14476, Golm, Germany
| | - Bo Zhang-Haagen
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Jülich Centre for Neutron Science & Institute of Complex Systems, Neutron Scattering (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Christina Decker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Bogdan Barz
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Mario Schneider
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science & Institute of Complex Systems, Neutron Scattering (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425, Jülich, Germany
- Jülich Centre for Neutron Science, Outstation at MLZ (JCNS-MLZ), Forschungszentrum Jülich, 85747, Garching, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science, Outstation at MLZ (JCNS-MLZ), Forschungszentrum Jülich, 85747, Garching, Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
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41
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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.
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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:
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42
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Condello C, Stöehr J. Aβ propagation and strains: Implications for the phenotypic diversity in Alzheimer's disease. Neurobiol Dis 2017; 109:191-200. [PMID: 28359847 DOI: 10.1016/j.nbd.2017.03.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/09/2017] [Accepted: 03/26/2017] [Indexed: 12/13/2022] Open
Abstract
The progressive nature of Alzheimer's disease (AD) is thought to occur, at least in part, by the self-replication and spreading of Aβ and Tau aggregates through a prion mechanism. Evidence now exists that structural variants of Aβ prions can propagate their distinct conformations through template-directed folding of naïve Aβ peptides. This notion implicates that the first self-propagating Aβ assembly to emerge in the brain dictates the conformation, anatomical spread and pace of subsequently formed deposits. It is hypothesized that a prion mechanism defines the molecular basis underlying the diverse clinicopathologic phenotypes observed across the spectrum of AD patients. Thus, distinct AD strains might require further sub-classification based on biochemical and structural characterization of aggregated Aβ. Here, we review the evidence for distinct, self-propagating Aβ strains, and discuss potential cellular mechanisms that might contribute to their manifestation. From this perspective, we also explore the implications of Aβ strains for current FDA-approved medical imaging probes and therapies for amyloid. Ultimately, the discovery of new molecular tools to differentiate Aβ strains and dissect the heterogeneity of AD may lead to the development of more informative diagnostics and strain-specific therapeutics.
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Affiliation(s)
- Carlo Condello
- Institute for Neurodegenerative Diseases, Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, United States
| | - Jan Stöehr
- Institute for Neurodegenerative Diseases, Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, United States.
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43
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Das P, Chacko AR, Belfort G. Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aβ 42 Dimer Structure. ACS Chem Neurosci 2017; 8:606-618. [PMID: 28292185 DOI: 10.1021/acschemneuro.6b00357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aβ dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aβ1-42 dimers have been performed, resulting into a total of 51 μs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aβ42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aβ42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.
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Affiliation(s)
- Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Anita R. Chacko
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Georges Belfort
- Howard
P. Isermann Department of Chemical and Biological Engineering, and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180-3590, United States
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44
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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
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45
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Petrushina I, Davtyan H, Hovakimyan A, Davtyan A, Passos GF, Cribbs DH, Ghochikyan A, Agadjanyan MG. Comparison of Efficacy of Preventive and Therapeutic Vaccines Targeting the N Terminus of β-Amyloid in an Animal Model of Alzheimer's Disease. Mol Ther 2017; 25:153-164. [PMID: 28129111 PMCID: PMC5363310 DOI: 10.1016/j.ymthe.2016.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 12/13/2022] Open
Abstract
Previously, we reported that Alzheimer's disease (AD) epitope vaccines (EVs) composed of N-terminal β-amyloid (Aβ42) B cell epitope fused with universal foreign T helper (Th) epitope(s) were immunogenic, potent, and safe in different amyloid precursor protein (APP) transgenic mice with early AD-like pathology. However, developing an effective therapeutic vaccine is much more challenging, especially when a self-antigen such as Aβ42 is a target. Here, we directly compare the efficacy of anti-Aβ42 antibodies in Tg2576 mice with low or high levels of AD-like pathology at the start of immunizations: 6-6.5 months for preventive vaccinations and 16-19 months for therapeutic vaccinations. EV in a preventive setting induced high levels of anti-Aβ antibodies, significantly reducing pathologic forms of Aβ in the brains of Tg2576 mice. When used therapeutically for immunesenescent Tg2576 mice, EV induced low levels of antibodies not sufficient for clearing of AD-like pathology. Separately, we demonstrated that EV was also not effective in 11-11.5-month-old Tg2576 mice with moderate AD-like pathology. However, we augmented the titers of anti-Aβ antibodies in transgenic (Tg) mice of the same age possessing the pre-existing memory Th cells and detected a significant decrease in diffuse and core plaques in cortical regions compared to control animals along with improved novel object recognition performance.
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Affiliation(s)
- Irina Petrushina
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Hayk Davtyan
- Department of Molecular Immunology, Institute for Molecular Medicine, Huntington Beach, CA 92647, USA
| | - Armine Hovakimyan
- Department of Molecular Immunology, Institute for Molecular Medicine, Huntington Beach, CA 92647, USA
| | - Arpine Davtyan
- Department of Molecular Immunology, Institute for Molecular Medicine, Huntington Beach, CA 92647, USA
| | - Giselle F Passos
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - David H Cribbs
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA
| | - Anahit Ghochikyan
- Department of Molecular Immunology, Institute for Molecular Medicine, Huntington Beach, CA 92647, USA.
| | - Michael G Agadjanyan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Immunology, Institute for Molecular Medicine, Huntington Beach, CA 92647, USA.
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46
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Ngo ST, Luu XC, Nguyen MT, Le CN, Vu VV. In silico studies of solvated F19W amyloid β (11–40) trimer. RSC Adv 2017. [DOI: 10.1039/c7ra07187f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
REMD studies shows that F19W mutation does not change in the overall structure of Aβ11–40 trimer significantly but increases it flexibility, consistent with the observed formation of the same fibril structures at slower rates.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Xuan-Cuong Luu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | | | - Chinh N. Le
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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47
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Nicolas G, Charbonnier C, Campion D. From Common to Rare Variants: The Genetic Component of Alzheimer Disease. Hum Hered 2016; 81:129-141. [PMID: 28002825 DOI: 10.1159/000452256] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/29/2016] [Indexed: 12/26/2022] Open
Abstract
Alzheimer disease (AD) is a remarkable example of genetic heterogeneity. Extremely rare variants in the APP, PSEN1, or PSEN2 genes, or duplications of the APP gene cause autosomal dominant forms, generally with complete penetrance by the age of 65 years. Nonautosomal dominant forms are considered as a complex disorder with a high genetic component, whatever the age of onset. Although genetically heterogeneous, AD is defined by the same neuropathological criteria in all configurations. According to the amyloid cascade hypothesis, the Aβ peptide, which aggregates in AD brains, is a key player. APP, PSEN1, or PSEN2 gene mutations increase the production of more aggregation-prone forms of the Aβ peptide, triggering the pathological process. Several risk factors identified in association studies hit genes involved in Aβ production/secretion, aggregation, clearance, or toxicity. Among them, the APOE ε4 allele is a rare example of a common allele with a large effect size, the ORs ranging from 4 to 11-14 for heterozygous and homozygous carriers, respectively. In addition, genome-wide association studies have identified more than two dozen loci with a weak but significant association, the OR of the at-risk allele ranging from 1.08 to 1.30. Recently, the use of massive parallel sequencing has enabled the analysis of rare variants in a genome-wide manner. Two rare variants have been nominally associated with AD risk or protection (TREM2 p.R47H, MAF approximately 0.002, OR approximately 4 and APP p.A673T, MAF approximately 0.0005, OR approximately 0.2). Association analyses at the gene level identified rare loss-of-function and missense, predicted damaging, variants (MAF <0.01) in the SORL1 and ABCA7 genes associated with a moderate relative risk (OR approximately 5 and approximately 2.8, respectively). Although the latter analyses revealed association signals with moderately rare variants by collapsing them, the power to detect genes hit by extremely rare variants is still limited. An alternative approach is to consider the de novo paradigm, stating that de novo variants may contribute to AD genetics in sporadic patients. Here, we critically review AD genetics reports with a special focus on rare variants.
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Affiliation(s)
- Gaël Nicolas
- CNR-MAJ, Rouen University Hospital, Rouen, France
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48
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Nguyen PH, Sterpone F, Pouplana R, Derreumaux P, Campanera JM. Dimerization Mechanism of Alzheimer Aβ 40 Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation. J Phys Chem B 2016; 120:12111-12126. [PMID: 27933940 DOI: 10.1021/acs.jpcb.6b10722] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Amyloid beta (Aβ) oligomerization is associated with the origin and progression of Alzheimer's disease (AD). While the A2V mutation enhances aggregation kinetics and toxicity, mixtures of wild-type (WT) and A2V, and also WT and A2T, peptides retard fibril formation and protect against AD. In this study, we simulate the equilibrium ensemble of WT:A2T Aβ40 dimer by means of extensive atomistic replica exchange molecular dynamics and compare our results with previous equivalent simulations of A2V:A2V, WT:WT, and WT:A2V Aβ40 dimers for a total time scale of nearly 0.1 ms. Qualitative comparison of the resulting thermodynamic properties, such as the relative binding free energies, with the reported experimental kinetic and thermodynamic data affords us important insight into the conversion from slow-pathway to fast-pathway dimer conformations. The crucial reaction coordinate or driving force of such transformation turns out to be related to hydrophobic interpeptide interactions. Analysis of the equilibrium ensembles shows that the fast-pathway conformations contain interpeptide out-of-register antiparallel β-sheet structures at short interpeptide distances. In contrast, the slow-pathway conformations are formed by the association of peptides at large interpeptide distances and high intrapeptide compactness, such as conformations containing intramolecular three-stranded β-sheets which sharply distinguish fast (A2V:A2V and WT:WT) and slow (WT:A2T and WT:A2V) amyloid-forming sequences. Also, this analysis leads us to predict that a molecule stabilizing the intramolecular three-stranded β-sheet or inhibiting the formation of an interpeptide β-sheet spanning residues 17-20 and 31-37 would further reduce fibril formation and probably the cytotoxicity of Aβ species.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Ramon Pouplana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , 08028 Barcelona, Catalonia, Spain
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité , 13 Rue Pierre et Marie Curie, 75005 Paris, France.,IUF (Institut Universitaire de France) , 103 Boulevard Michel, 75005 Paris, France
| | - Josep M Campanera
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , 08028 Barcelona, Catalonia, Spain
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49
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Chiricotto M, Tran TT, Nguyen PH, Melchionna S, Sterpone F, Derreumaux P. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mara Chiricotto
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Thanh Thuy Tran
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Simone Melchionna
- Istituto Sistemi Complessi; Consiglio Nazionale delle Ricerche; P. le A. Moro 2 00185 Rome Italy
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
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50
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Nguyen PH, Sterpone F, Campanera JM, Nasica-Labouze J, Derreumaux P. Impact of the A2V Mutation on the Heterozygous and Homozygous Aβ1-40 Dimer Structures from Atomistic Simulations. ACS Chem Neurosci 2016; 7:823-32. [PMID: 27007027 DOI: 10.1021/acschemneuro.6b00053] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The A2V mutation was reported to protect from Alzheimer's disease in its heterozygous form and cause an early Alzheimer's disease type dementia in its homozygous form. Experiments showed that the aggregation rate follows the order A2V > WT (wild-type) > A2V-WT. To understand the impact of this mutation, we carried out replica exchange molecular dynamics simulations of Aβ1-40 WT-A2V and A2V-A2V dimers and compared to the WT dimer. Our atomistic simulations reveal that the mean secondary structure remains constant, but there are substantial differences in the intramolecular and intermolecular conformations upon single and double A2V mutation. Upon single mutation, the intrinsic disorder is reduced, the intermolecular potential energies are reduced, the population of intramolecular three-stranded β-sheets is increased, and the number of all α dimer topologies is decreased. Taken together, these results offer an explanation for the reduced aggregation rate of the Aβ1-40 A2V-WT peptides and the protective effect of A2V in heterozygotes.
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Affiliation(s)
- Phuong H. Nguyen
- Laboratoire de
Biochimie Théorique, UPR 9080 CNRS, Université Paris
Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de
Biochimie Théorique, UPR 9080 CNRS, Université Paris
Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Josep M. Campanera
- Departament
de Fisicoquimica, Facultat de Farmacia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Jessica Nasica-Labouze
- Laboratoire de
Biochimie Théorique, UPR 9080 CNRS, Université Paris
Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de
Biochimie Théorique, UPR 9080 CNRS, Université Paris
Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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