1
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Nguyen PH, Derreumaux P. An S-Shaped Aβ42 Cross-β Hexamer Embedded into a Lipid Bilayer Reveals Membrane Disruption and Permeability. ACS Chem Neurosci 2023; 14:936-946. [PMID: 36757886 DOI: 10.1021/acschemneuro.2c00785] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The interactions of amyloid oligomers with membranes are known to contribute to cellular toxicity. Numerous in vitro experimental studies reported on the insertion of oligomers of different sizes that can induce cell membrane disruption, extract lipids, and form ion-permeable transmembrane pores. The current repertoire of amyloid-beta (Aβ) membrane-inserted folds that was subject to high-resolution structure NMR spectroscopy and computer simulations is devoid of any cross-β fibrillar structure. In this study, we explored the dynamics of an S-shaped Aβ42 cross-β hexamer model inserted into a lipid bilayer membrane by two atomistic molecular dynamics simulations. The initial model is characterized by the hydrophobic residues at the central hydrophobic core (residues 17-21, CHC) and the C-terminus (residues 30-42) embedded into the membrane. We observed major structural secondary, tertiary, and quaternary rearrangements leading to two distinct species, hexamer and two trimers, accompanied by membrane disruption and water permeation. The simulations show that some configurations, but not the majority, have the CHC and C-terminus hydrophobic residues exposed to the solvent. Overall, our computational results offer new perspectives to understand the relationship between Aβ42 assemblies and membrane permeability.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Fondation Edmond de Rothschild, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Fondation Edmond de Rothschild, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.,Institut Universitaire de France (IUF), 75005 Paris, France
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2
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Khayat E, Delfing BM, Laracuente X, Olson A, Lockhart C, Klimov DK. Lysine Acetylation Changes the Mechanism of Aβ25-35 Peptide Binding and Dimerization in the DMPC Bilayer. ACS Chem Neurosci 2023; 14:494-505. [PMID: 36656569 DOI: 10.1021/acschemneuro.2c00722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The impact of Lys28 acetylation on Alzheimer's Aβ peptide binding to the lipid bilayer has not been previously studied, either experimentally or computationally. To probe this common post-translational modification, we performed all-atom replica exchange molecular dynamics simulations targeting binding and aggregation of acetylated acAβ25-35 peptide within the DMPC bilayer. Using the unmodified Aβ25-35 studied previously as a reference, our results can be summarized as follows. First, Lys28 acetylation strengthens the Aβ25-35 hydrophobic moment and consequently promotes the helical structure across the peptide extending it into the N-terminus. Second, because Lys28 acetylation disrupts electrostatic contact between Lys28 and lipid phosphate groups, it reduces the binding affinity of acAβ25-35 peptides to the DMPC bilayer. Accordingly, although acetylation preserves the bimodal binding featuring a preferred inserted state and a less probable surface bound state, it decreases the stability of the former. Third, acetylation promotes acAβ25-35 aggregation and eliminates monomers as thermodynamically viable species. More importantly, acAβ25-35 retains as the most thermodynamically stable the inserted dimer with unique head-to-tail helical aggregation interface. However, due to enhanced helix structure, this dimer state becomes less stable and is less likely to propagate into higher order aggregates. Thus, acetylation is predicted to facilitate the formation of low-molecular-weight oligomers. Other post-translational modifications, including phosphorylation and oxidation, reduce helical propensity and have divergent impact on aggregation. Consequently, acetylation, when considered in its totality, has distinct consequences on Aβ25-35 binding and aggregation in the lipid bilayer.
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Affiliation(s)
- Elias Khayat
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Bryan M Delfing
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Xavier Laracuente
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Audrey Olson
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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3
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Navakauskas E, Niaura G, Strazdaite S. Effect of deuteration on a phosphatidylcholine lipid monolayer structure: New insights from vibrational sum-frequency generation spectroscopy. Colloids Surf B Biointerfaces 2022; 220:112866. [PMID: 36174490 DOI: 10.1016/j.colsurfb.2022.112866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/07/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2022]
Abstract
We used vibrational sum-frequency generation (VSFG) spectroscopy to elucidate the possible effect of various levels of isotopic substitution (H/D) on the properties of the DPPC monolayer by probing DPPC/D2O interface. We found that deuteration of the choline group has a great impact on monolayer properties, while monolayers with deuterated alkyl chains do not exhibit any differences under our experimental conditions. In addition, deuteration of the choline group strongly affected the hydration of the phosphate group. We showed by probing symmetric stretching vibration of phosphate group that denser packing only slightly reduced the hydration of DPPC-d13 and DPPC-d75 monolayers. Moreover, addition of calcium ions, which generally cause a marked dehydration of the lipid monolayer, had no effect on lipid monolayers with deuterated choline group. We proposed that one way to explain this experimental finding could be deuteration induced changes in the structure of lipid's choline group, resulting in a well-hydrated but Ca2+ ion blocking structure. These results have important implications for various spectroscopic techniques, which commonly use deuteration of phospholipids to circumvent overlapping between vibrational bands.
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Affiliation(s)
- Edvinas Navakauskas
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Saulėtekis ave. 3, LT-10257 Vilnius, Lithuania
| | - Gediminas Niaura
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Saulėtekis ave. 3, LT-10257 Vilnius, Lithuania.
| | - Simona Strazdaite
- Department of Organic Chemistry, Center for Physical Sciences and Technology (FTMC), Saulėtekis ave. 3, LT-10257 Vilnius, Lithuania
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4
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Jaragh-Alhadad LA, Falahati M. Tin oxide nanoparticles trigger the formation of amyloid β oligomers/protofibrils and underlying neurotoxicity as a marker of Alzheimer's diseases. Int J Biol Macromol 2022; 204:154-160. [PMID: 35124024 DOI: 10.1016/j.ijbiomac.2022.01.190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/11/2022] [Accepted: 01/29/2022] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is known as one of the most common forms of dementia, and oligomerization of amyloid β (Aβ42) peptides can result in the onset of AD. Tin oxide nanoparticles (SnO2 NPs) showed several applications in biomedical fields can trigger unwanted interaction with proteins and inducing protein aggregation. Herein, we synthesized SnO2 NPs via the hydrothermal method and characterized by UV-visible, XRD, FTIR, TEM, and DLS techniques. Afterward, the formation of Aβ42 amyloid oligomers/protofibrils treated alone and with SnO2 NPs was explored by ThT and Nile red fluorescence and CD spectroscopic methods along with TEM imaging. The neurotoxicity of different spices of Aβ42 samples against PC-12 cells was then explored by MTT and caspase-3 activity assays. The characterization of SnO2 NPs confirmed the successful synthesis of crystalline NPs (20-30 nm). Different biophysical and cellular analyses indicated that SnO2 NPs accelerated Aβ42 fibrillogenesis and promoted amyloid oligomers/protofibrils cytotoxicity. As compared to the Aβ42 samples grown alone, the ThT and ANS fluorescence intensity along with ellipticity results indicated the promotory effect of SnO2 NPs on the formation of oligomers/protofibrils. Also, the cellular results showed that the treated Aβ42 samples with SnO2 NPs further reduced cell viability through activation of caspase-3. In conclusion, SnO2 NPs greatly accelerate the fibrillation of Aβ42 peptides and lead to the formation of more toxic species. The present data may offer further warrants into nano-based systems for biomedical applications in the central nervous system.
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Affiliation(s)
- Laila Abdulmohsen Jaragh-Alhadad
- Department of Chemistry, College of Science, Kuwait University, Safat 13060, Kuwait; Cardiovascular and Metabolic Sciences Department, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA.
| | - Mojtaba Falahati
- Laboratory Experimental Oncology and Nanomedicine Innovation Center Erasmus (NICE), Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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5
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Sant V, Som M, Karkisaval AG, Carnahan P, Lal R. Scavenging amyloid oligomers from neurons with silica nanobowls: Implications for amyloid diseases. Biophys J 2021; 120:3329-3340. [PMID: 34242592 PMCID: PMC8391079 DOI: 10.1016/j.bpj.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/20/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
Amyloid-β (Aβ) oligomers are toxic species implicated in Alzheimer's disease (AD). The prevailing hypothesis implicates a major role of membrane-associated amyloid oligomers in AD pathology. Our silica nanobowls (NB) coated with lipid-polymer have submicromolar affinity for Aβ binding. We demonstrate that NB scavenges distinct fractions of Aβs in a time-resolved manner from amyloid precursor protein-null neuronal cells after incubation with Aβ. At short incubation times in cell culture, NB-Aβ seeds have aggregation kinetics resembling that of extracellular fraction of Aβ, whereas at longer incubation times, NB-Aβ seeds scavenge membrane-associated Aβ. Aβ aggregates can be eluted from NB surfaces by mechanical agitation and appear to retain their aggregation driving domains as seen in seeding aggregation experiments. These results demonstrate that the NB system can be used for time-resolved separation of toxic Aβ species from biological samples for characterization and in diagnostics. Scavenging membrane-associated amyloids using lipid-functionalized NB without chemical manipulation has wide applications in the diagnosis and therapy of AD and other neurodegenerative diseases, cancer, and cardiovascular conditions.
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Affiliation(s)
- Vrinda Sant
- Materials Science and Engineering, University of California San Diego, La Jolla, California.
| | - Madhura Som
- Department of Nanoengineering, University of California San Diego, La Jolla, California
| | - Abhijith G Karkisaval
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California
| | - Parker Carnahan
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Ratnesh Lal
- Materials Science and Engineering, University of California San Diego, La Jolla, California; Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California.
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6
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Ngo ST, Nguyen PH, Derreumaux P. Impact of the Rat R5G, Y10F, and H13R Mutations on Tetrameric Aβ42 β-Barrel in a Lipid Bilayer Membrane Model. J Phys Chem B 2021; 125:3105-3113. [PMID: 33739113 DOI: 10.1021/acs.jpcb.1c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three amino acid substitutions distinguish rat and human Aβ42 peptides and contribute to the difference in toxicity properties. Indeed, aged rodents rarely develop the characteristic lesions of Alzheimer's disease in contrast to humans. Both peptides form, however, amyloid fibrils in buffer solution, but their affinities to the membrane vary. In particular, there is experimental evidence that the rat Aβ42 peptide does not induce Ca2+ fluxes in cells. We recently designed a tetrameric β-barrel structure and showed that this model is severely destabilized for Aβ40 human compared to its Aβ42 human counterpart, explaining the absence of ionic currents of Aβ40 in planar lipid bilayers. In this study, we asked whether our model is destabilized for the rat Aβ42 peptide by using extensive replica exchange molecular dynamics simulation in a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer membrane. Our results show that the much lower propensity of aged rodents to develop Alzheimer's disease symptoms might be correlated to its tetrameric β-barrel stability in the cell membrane.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, 13 rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, 13 rue Pierre et Marie Curie, 75005 Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France.,Laboratory of Theoretical Chemistry and Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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7
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Deo T, Cheng Q, Paul S, Qiang W, Potapov A. Application of DNP-enhanced solid-state NMR to studies of amyloid-β peptide interaction with lipid membranes. Chem Phys Lipids 2021; 236:105071. [PMID: 33716023 DOI: 10.1016/j.chemphyslip.2021.105071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/13/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022]
Abstract
The cellular membrane disruption induced by the aggregation of Aβ peptide has been proposed as a plausible cause of neuronal cell death during Alzheimer's disease. The molecular-level details of the Aβ interaction with cellular membranes were previously probed using solid state NMR (ssNMR), however, due to the limited sensitivity of the latter, studies were limited to samples with high Aβ-to-lipid ratio. The dynamic nuclear polarization (DNP) is a technique for increasing the sensitivity of NMR. In this work we demonstrate the feasibility of DNP-enhanced ssNMR studies of Aβ40 peptide interacting with various model liposomes: (1) a mixture of zwitterionic 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) and negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG); (2) a mixture of POPC, POPG, cholesterol, sphingomyelin and ganglioside GM1; (3) the synaptic plasma membrane vesicles (SPMVs) extracted from rat brain tissues. In addition, DNP-ssNMR was applied to capturing changes in Aβ40 conformation taking place upon the peptide insertion into POPG liposomes. The signal enhancements under conditions of DNP allow carrying out informative 2D ssNMR experiments with about 0.25 mg of Aβ40 peptides (i.e. reaching Aβ40-to-lipid ratio of 1:200). In the studied liposome models, the 13C NMR chemical shifts at many 13C-labelled sites of Aβ40 are characteristic of β-sheets. In addition, in POPG liposomes the peptide forms hydrophobic contacts F19-L34 and F19-I32. Both the chemical shifts and hydrophobic contacts of Aβ40 in POPG remain the same before and after 8 h of incubation. This suggests that conformation at the 13C-labelled sites of the peptide is similar before and after the insertion process. Overall, our results demonstrate that DNP helps to overcome the sensitivity limitation of ssNMR, and thereby expand the applicability of ssNMR for charactering the Aβ peptide interacting with lipids.
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Affiliation(s)
- Thomas Deo
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Qinghui Cheng
- Department of Chemistry, Binghamton University, the State University of New York, Binghamton, NY, 13902, USA
| | - Subhadip Paul
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Wei Qiang
- Department of Chemistry, Binghamton University, the State University of New York, Binghamton, NY, 13902, USA
| | - Alexey Potapov
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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8
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Rissanou AN, Keliri A, Arnittali M, Harmandaris V. Self-assembly of diphenylalanine peptides on graphene via detailed atomistic simulations. Phys Chem Chem Phys 2021; 22:27645-27657. [PMID: 33283818 DOI: 10.1039/d0cp03671d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom molecular dynamics simulations. Two interfacial systems are studied, with different concentrations of dipeptides and the results are compared with an aqueous solution of FF at room temperature. Corresponding length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface. A hierarchical formation of FF structures is observed involving two sequential processes: first, a stabilized interfacial layer of dipeptides onto the graphene surface is formulated, which next is followed by the development of a structure of self-aggregated dipeptides on top of this layer. The whole procedure is completed in almost 200 ns, whereas self-assembly in the system without graphene is accomplished much faster; in less than 50 ns cylindrical structures, the microscopic signal of the macroscopic fibrillar ones, are formed. Strong π-π* interactions between FF and the graphene lead to a parallel orientation to the graphene layer of the phenyl rings within a characteristic time of 80 ns, similar to the one indicated by the time evolution of the number of adsorbed FF atoms at the surface. Reduction in the number of hydrogen bonds between FF peptides is observed because of the graphene layer, since it disturbs their self-assembly propensity. The self-assembly of dipeptides and their adsorption onto the graphene surface destruct the hydrogen bond network of water, in the vicinity of FF, however, the total number of hydrogen bonds in all systems increases, promoting the formed structures.
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Affiliation(s)
- Anastassia N Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas, (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
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9
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Karkisaval AG, Rostagno A, Azimov R, Ban DK, Ghiso J, Kagan BL, Lal R. Ion channel formation by N-terminally truncated Aβ (4-42): relevance for the pathogenesis of Alzheimer's disease. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 29:102235. [PMID: 32531337 DOI: 10.1016/j.nano.2020.102235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 11/17/2022]
Abstract
Aβ deposition is a pathological hallmark of Alzheimer's disease (AD). Besides the full-length amyloid forming peptides (Aβ1-40 and Aβ1-42), biochemical analyses of brain deposits have identified a variety of N- and C-terminally truncated Aβ variants in sporadic and familial AD patients. However, their relevance for AD pathogenesis remains largely understudied. We demonstrate that Aβ4-42 exhibits a high tendency to form β-sheet structures leading to fast self-aggregation and formation of oligomeric assemblies. Atomic force microscopy and electrophysiological studies reveal that Aβ4-42 forms highly stable ion channels in lipid membranes. These channels that are blocked by monoclonal antibodies specifically recognizing the N-terminus of Aβ4-42. An Aβ variant with a double truncation at phenylalanine-4 and leucine 34, (Aβ4-34), exhibits unstable channel formation capability. Taken together the results presented herein highlight the potential benefit of C-terminal proteolytic cleavage and further support an important pathogenic role for N-truncated Aβ species in AD pathophysiology.
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Affiliation(s)
- Abhijith G Karkisaval
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, 92092, USA
| | - Agueda Rostagno
- Department of Pathology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY, 10016, USA
| | - Rustam Azimov
- Department of Psychiatry, Geffen School of Medicine, University of California, Los Angeles, California 90095, USA; Semel Neuropsychiatric for Neuroscience & Human Behavior, University of California, Los Angeles, California 90095, United States
| | - Deependra K Ban
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, 92092, USA
| | - Jorge Ghiso
- Department of Pathology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY, 10016, USA; Department of Psychiatry, New York University Grossman School of Medicine, 550 First Avenue, New York, NY, 10016, USA.
| | - Bruce L Kagan
- Department of Psychiatry, Geffen School of Medicine, University of California, Los Angeles, California 90095, USA; Semel Neuropsychiatric for Neuroscience & Human Behavior, University of California, Los Angeles, California 90095, United States.
| | - Ratnesh Lal
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, 92092, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, 92092, USA; Materials Science and Engineering, University of California San Diego, La Jolla, California, 92092, USA.
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10
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Younger S, Jang H, Davies HA, Niemiec MJ, Garcia JGN, Nussinov R, Migrino RQ, Madine J, Arce FT. Medin Oligomer Membrane Pore Formation: A Potential Mechanism of Vascular Dysfunction. Biophys J 2020; 118:2769-2782. [PMID: 32402244 PMCID: PMC7264854 DOI: 10.1016/j.bpj.2020.04.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/11/2020] [Accepted: 04/17/2020] [Indexed: 12/12/2022] Open
Abstract
Medin, a 50-amino-acid cleavage product of the milk fat globule-EGF factor 8 protein, is one of the most common forms of localized amyloid found in the vasculature of individuals older than 50 years. Medin induces endothelial dysfunction and vascular inflammation, yet despite its prevalence in the human aorta and multiple arterial beds, little is known about the nature of its pathology. Medin oligomers have been implicated in the pathology of aortic aneurysm, aortic dissection, and more recently, vascular dementia. Recent in vitro biomechanical measurements found increased oligomer levels in aneurysm patients with altered aortic wall integrity. Our results suggest an oligomer-mediated toxicity mechanism for medin pathology. Using lipid bilayer electrophysiology, we show that medin oligomers induce ionic membrane permeability by pore formation. Pore activity was primarily observed for preaggregated medin species from the growth-phase and rarely for lag-phase species. Atomic force microscopy (AFM) imaging of medin aggregates at different stages of aggregation revealed the gradual formation of flat domains resembling the morphology of supported lipid bilayers. Transmission electron microscopy images showed the coexistence of compact oligomers, largely consistent with the AFM data, and larger protofibrillar structures. Circular dichroism spectroscopy revealed the presence of largely disordered species and suggested the presence of β-sheets. This observation and the significantly lower thioflavin T fluorescence emitted by medin aggregates compared to amyloid-β fibrils, along with the absence of amyloid fibers in the AFM and transmission electron microscopy images, suggest that medin aggregation into pores follows a nonamyloidogenic pathway. In silico modeling by molecular dynamics simulations provides atomic-level structural detail of medin pores with the CNpNC barrel topology and diameters comparable to values estimated from experimental pore conductances.
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Affiliation(s)
- Scott Younger
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona
| | - Hyunbum Jang
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Hannah A Davies
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Martin J Niemiec
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona
| | - Joe G N Garcia
- Department of Medicine, University of Arizona, Tucson, Arizona
| | - Ruth Nussinov
- Computational Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raymond Q Migrino
- Office of Research, Phoenix Veterans Affairs Health Care System, Phoenix, Arizona; Department of Medicine, University of Arizona College of Medicine-Phoenix, Arizona
| | - Jillian Madine
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Fernando T Arce
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona; Department of Medicine, University of Arizona, Tucson, Arizona.
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11
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Li Y, Li N, Wang L, Lu Q, Ji X, Zhang F. A Comparative Study on the Self-Assembly of Peptide TGV-9 by In Situ Atomic Force Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:319-325. [PMID: 32051052 DOI: 10.1017/s1431927620000082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Previous studies of amyloid diseases reported that the aggregating proteins share a similar conserved peptide sequence which can form the cross-β-sheet-containing nanostructures like nanofilaments. The template-assisted self-assembly (TASA) of peptides on inorganic substrates with different hydrophilicity could be an alternative approach to shed light on the fibrillization mechanism of proteins/peptides in vivo. To figure out the effect of interfaces on amyloid aggregation, we herein employed in situ atomic force microscopy (AFM) to investigate the self-assembling of a Parkinson disease-related core peptide sequence (TGV-9) on a hydrophobic liquid-solid interface via real-time observation of the dynamic fibrillization process. The results show that TGV-9 forms one-dimensional nanostructures on the surface of highly ordered pyrolytic graphite (HOPG) with three preferred growth orientations, which are consistent with the atomic lattice of HOPG, indicating an epitaxial growth or TASA. Conversely, the nanostructures formed in bulk solution can be free-standing nanofilaments, and the fibrillization mechanism is different from that on HOPG. These results could not only deepen the understanding of the protein/peptide aggregation mechanism but also benefit for the early diagnosis and clinic treatment of related diseases.
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Affiliation(s)
- Yaping Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Na Li
- Terahertz Technology Innovation Research Institute, Shanghai Key Laboratory of Modern Optical System, Terahertz Science Cooperative Innovation Center, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai200093, P. R. China
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, Hohhot010018, P. R. China
| | - Lei Wang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Qinhua Lu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Xiang Ji
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
| | - Feng Zhang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou014010, P. R. China
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, Hohhot010018, P. R. China
- Key Laboratory of Oral Medicine, Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Institute of Oral Disease, Stomatology Hospital, Guangzhou Medical University, Guangzhou511436, P. R. China
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12
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Xing Y, Sun Y, Wang B, Ding F. Morphological Determinants of Carbon Nanomaterial-Induced Amyloid Peptide Self-Assembly. Front Chem 2020; 8:160. [PMID: 32211382 PMCID: PMC7076083 DOI: 10.3389/fchem.2020.00160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/24/2020] [Indexed: 01/12/2023] Open
Abstract
Hybridizing carbon nanomaterials (CNMs) with amyloid fibrils—the ordered nanostructures self-assembled by amyloidogenic peptides—has found promising applications in bionanotechology. Understanding fundamental interactions of CNMs with amyloid peptides and uncovering the determinants of their self-assembly structures and dynamics are, therefore, pivotal for enriching and enabling this novel class of hybrid nanomaterials. Here, we applied atomistic molecular dynamics simulations to investigate the self-assembly of two amyloid peptides—the amyloidogenic core residues 16-22 of amyloid-β (Aβ16−22) and the non-amyloid-β core of α-synuclein (NACore68−78)—on the surface of carbon nanotubes (CNT) with different sizes and chirality. Our computational results showed that with small radial CNTs, both types of peptides could form β-sheets wrapping around the nanotube surface into a supercoiled morphology. The angle between β-strands and nanotube axes in the supercoil structure depended mainly on the peptide sequence and CNT radius, but also weakly on the CNT chirality. Large radial CNTs and the extreme case of the flat graphene nanosheet, on the other hand, could nucleate amyloid fibrils perpendicular to the surface. Our results provided new insights of hybridizing CNMs with amyloid peptides and also offered a novel approach to manipulate the morphology of CNM-induced amyloid assembly by tuning the surface curvature, peptide sequence, and molecular ratio between peptides and available CNM surface area, which may be useful in engineering nanocomposites with high-order structures.
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Affiliation(s)
- Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Bo Wang
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
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13
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Martinez Hernandez A, Urbanke H, Gillman AL, Lee J, Ryazanov S, Agbemenyah HY, Benito E, Jain G, Kaurani L, Grigorian G, Leonov A, Rezaei-Ghaleh N, Wilken P, Arce FT, Wagner J, Fuhrmann M, Caruana M, Camilleri A, Vassallo N, Zweckstetter M, Benz R, Giese A, Schneider A, Korte M, Lal R, Griesinger C, Eichele G, Fischer A. The diphenylpyrazole compound anle138b blocks Aβ channels and rescues disease phenotypes in a mouse model for amyloid pathology. EMBO Mol Med 2019; 10:32-47. [PMID: 29208638 PMCID: PMC5760857 DOI: 10.15252/emmm.201707825] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease is a devastating neurodegenerative disease eventually leading to dementia. An effective treatment does not yet exist. Here we show that oral application of the compound anle138b restores hippocampal synaptic and transcriptional plasticity as well as spatial memory in a mouse model for Alzheimer's disease, when given orally before or after the onset of pathology. At the mechanistic level, we provide evidence that anle138b blocks the activity of conducting Aβ pores without changing the membrane embedded Aβ-oligomer structure. In conclusion, our data suggest that anle138b is a novel and promising compound to treat AD-related pathology that should be investigated further.
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Affiliation(s)
- Ana Martinez Hernandez
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Department for Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Hendrik Urbanke
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Alan L Gillman
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joon Lee
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sergey Ryazanov
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Hope Y Agbemenyah
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Eva Benito
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Gaurav Jain
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Lalit Kaurani
- DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Gayane Grigorian
- Department of Cellular Neurobiology, Technical University Braunschweig, Braunschweig, Germany
| | - Andrei Leonov
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Nasrollah Rezaei-Ghaleh
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Translational Structural Biology of Dementia, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Petra Wilken
- DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.,Group for Translational Research in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Fernando Teran Arce
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jens Wagner
- Group for Neuroimmunology and Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Martin Fuhrmann
- Group for Neuroimmunology and Imaging, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Mario Caruana
- Department of Physiology and Biochemistry, Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Angelique Camilleri
- Department of Physiology and Biochemistry, Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Markus Zweckstetter
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Department of Translational Structural Biology of Dementia, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.,Department of Neurology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Roland Benz
- Life Sciences and Chemistry, Jacobs University of Bremen, Bremen, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Anja Schneider
- DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany.,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.,Group for Translational Research in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE) Göttingen, Göttingen, Germany
| | - Martin Korte
- Department of Cellular Neurobiology, Technical University Braunschweig, Braunschweig, Germany .,Helmholtz Center for Infections Research, Braunschweig, Germany
| | - Ratnesh Lal
- Department of Bioengineering, Materials Science and Engineering, Department of Mechanical and Aerospace Engineering and Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Christian Griesinger
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany .,DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain, Göttingen, Germany
| | - Gregor Eichele
- Department for Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Andre Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany .,Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
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14
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15
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Li C, Qin R, Liu R, Miao S, Yang P. Functional amyloid materials at surfaces/interfaces. Biomater Sci 2018; 6:462-472. [PMID: 29435550 DOI: 10.1039/c7bm01124e] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With the development of nanotechnology, functional amyloid materials are drawing increasing attention, and numerous remarkable applications are emerging. Amyloids, defined as a class of supramolecular assemblies of misfolded proteins or peptides into β-sheet fibrils, have evolved in many new respects and offer abundant chemical/biological functions. These proteinaceous micro/nano-structures provide excellent biocompatibility, rich phase behaviours, strong mechanical properties, and stability at interfaces not only in nature but also in functional materials, displaying versatile interactions with surfaces/interfaces that have been widely adopted in bioadhesion, synthetic biology, and composites. Overall, functional amyloids at surfaces/interfaces have excellent potential applications in next-generation biotechnology and biomaterials.
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Affiliation(s)
- Chen Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Xi'an 710119, China.
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16
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Choi H, Yoon T, Na S. Length-Dependent Manifestation of Vibration Modes Regulates a Specific Intermediate Morphology of Aβ17-42 in Different Environments. Chemphyschem 2018; 19:1643-1654. [PMID: 29575445 DOI: 10.1002/cphc.201800010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Indexed: 12/25/2022]
Abstract
Various cytotoxic mechanisms for neurodegenerative disease are induced by specific conformations of Aβ intermediates. The efforts to understand the diverse intermediate forms of amyloid oligomers have been focused on understanding the aggregation mechanism of specific morphologies for Aβ intermediates. However, these are still not easy tasks to be accomplished because the diverse conformations of Aβ intermediates can be altered during the aggregation process, even though the same Aβ monomers are present. Thus, efforts to reveal the conformational change mechanism could be a fundamental process to understand the formation of diverse Aβ intermediate conformations. Here, we evaluate the conformational characteristics of Aβ17-42 fibrillar oligomers in different environments according to the length. We observed that Aβ fibrillar oligomers optimize their inherent hydrogen bonds and configurational entropy to stabilize their structure according to the simulation time and their length increase. In addition, we revealed the role of the expressed vibration mode shape in the fibrillar oligomers' elongation and deformation processes. Our results suggest that limitations in amyloid oligomer growth and transformations of their morphologies can be regulated and controlled by modifying the vibration features.
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Affiliation(s)
- Hyunsung Choi
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Taeyoung Yoon
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul, 02841, Republic of Korea
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17
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Zhang M, Zhai Q, Wan L, Chen L, Peng Y, Deng C, Xiang J, Yan J. Electrochemical Impedance Spectroscopy for Real-Time Detection of Lipid Membrane Damage Based on a Porous Self-Assembly Monolayer Support. Anal Chem 2018; 90:7422-7427. [DOI: 10.1021/acs.analchem.8b00884] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Meng Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Qingyu Zhai
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Liping Wan
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Li Chen
- State Key Laboratory of Physical Chemistry of the Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yu Peng
- State Key Laboratory of Physical Chemistry of the Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Chunyan Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Juan Xiang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jiawei Yan
- State Key Laboratory of Physical Chemistry of the Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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18
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Niu Z, Zhang Z, Zhao W, Yang J. Interactions between amyloid β peptide and lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1663-1669. [PMID: 29679539 DOI: 10.1016/j.bbamem.2018.04.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
Abstract
The presence of amyloid plaques in the brain is a typical characteristic of Alzheimer's disease (AD). Amyloid plaques are formed from the deposits of aggregated amyloid β peptide (Aβ). The toxicity induced by Aβ aggregates is correlated with Aβ-membrane interactions. The mutual influences between aggregation and membranes are complicated and unclear. In recent years advanced experiments and findings are emerging to give us more detailed information on Aβ-membrane interactions. In this review, we mainly focus on the Aβ-membrane interactions and membrane-induced Aβ structures. The mechanism of Aβ-membrane interactions is also summarized, which provides insights into the prevention and treatment of AD.
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Affiliation(s)
- Zheng Niu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 430071 Wuhan, PR China
| | - Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 430071 Wuhan, PR China
| | - Weijing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 430071 Wuhan, PR China
| | - Jun Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, 430071 Wuhan, PR China.
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19
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Liu Y, Ren B, Zhang Y, Sun Y, Chang Y, Liang G, Xu L, Zheng J. Molecular simulation aspects of amyloid peptides at membrane interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1906-1916. [PMID: 29421626 DOI: 10.1016/j.bbamem.2018.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022]
Abstract
The interactions of amyloid peptides with cell membranes play an important role in maintaining the integrity and functionality of cell membrane. A thorough molecular-level understanding of the structure, dynamics, and interactions between amyloid peptides and cell membranes is critical to amyloid aggregation and toxicity mechanisms for the bench-to-bedside applications. Here we review the most recent computational studies of amyloid peptides at model cell membranes. Different mechanisms of action of amyloid peptides on/in cell membranes, targeted by different computational techniques at different lengthscales and timescales, are rationally discussed. Finally, we have proposed some new insights into the remaining challenges and perspectives for future studies to improve our understanding of the activity of amyloid peptides associated with protein-misfolding diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Yonglan Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yung Chang
- R&D Center for Membrane Technology and Department of Chemical EngineeringChung Yuan Christian University, Chung-Li, Taoyuan 320, Taiwan
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Lijian Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
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20
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Karaballi RA, Merchant S, Power SR, Brosseau CL. Electrochemical surface-enhanced Raman spectroscopy (EC-SERS) study of the interaction between protein aggregates and biomimetic membranes. Phys Chem Chem Phys 2018; 20:4513-4526. [DOI: 10.1039/c7cp06838g] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
EC-SERS is used for the first time to characterize protein aggregate–biomembrane interactions.
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Affiliation(s)
| | | | - Sasha R. Power
- Department of Chemistry
- Saint Mary's University
- Halifax
- Canada
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21
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Li N, Jang H, Yuan M, Li W, Yun X, Lee J, Du Q, Nussinov R, Hou J, Lal R, Zhang F. Graphite-Templated Amyloid Nanostructures Formed by a Potential Pentapeptide Inhibitor for Alzheimer's Disease: A Combined Study of Real-Time Atomic Force Microscopy and Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6647-6656. [PMID: 28605901 PMCID: PMC7900909 DOI: 10.1021/acs.langmuir.7b00414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly of peptides is closely related to many diseases, including Alzheimer's, Parkinson's, and prion diseases. Understanding the basic mechanism of this assembly is essential for designing ultimate cure and preventive measures. Template-assisted self-assembly (TASA) of peptides on inorganic substrates can provide fundamental understanding of substrate-dependent peptides assemble, including the role of hydrophobic interface on the peptide fibrillization. Here, we have studied the self-assembly process of a potential pentapeptide inhibitor on the surface of highly oriented pyrolytic graphite (HOPG) using real time atomic force microscopy (RT-AFM) as well as molecular dynamics (MD) simulation. Experimental and simulation results show nanofilament formation consisting of β-sheet structures and epitaxial growth on HOPG. Height analysis of the nanofilaments and MD simulation indicate that the peptides adopt a lying down configuration of double-layered antiparallel β-sheets for its epitaxial growth, and the number of nanofilament layers is concentration-dependent. These findings provide new perspective for the mechanism of peptide-based fibrillization in amyloid diseases as well as for designing well-ordered micrometrical and nanometrical structures.
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Affiliation(s)
- Na Li
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
| | - Ming Yuan
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Wanrong Li
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Xiaolin Yun
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Joon Lee
- Materials Science and Engineering Program and Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
| | - Qiqige Du
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jiahua Hou
- Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Ratnesh Lal
- Materials Science and Engineering Program and Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
| | - Feng Zhang
- Agricultural Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 United States
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22
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Lee J, Kim YH, T Arce F, Gillman AL, Jang H, Kagan BL, Nussinov R, Yang J, Lal R. Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts. ACS Chem Neurosci 2017; 8:1348-1357. [PMID: 28135799 PMCID: PMC6197823 DOI: 10.1021/acschemneuro.7b00006] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Amyloid β (Aβ) oligomers are the predominant toxic species in the pathology of Alzheimer's disease. The prevailing mechanism for toxicity by Aβ oligomers includes ionic homeostasis destabilization in neuronal cells by forming ion channels. These channel structures have been previously studied in model lipid bilayers. In order to gain further insight into the interaction of Aβ oligomers with natural membrane compositions, we have examined the structures and conductivities of Aβ oligomers in a membrane composed of brain total lipid extract (BTLE). We utilized two complementary techniques: atomic force microscopy (AFM) and black lipid membrane (BLM) electrical recording. Our results indicate that Aβ1-42 forms ion channel structures in BTLE membranes, accompanied by a heterogeneous population of ionic current fluctuations. Notably, the observed current events generated by Aβ1-42 peptides in BTLE membranes possess different characteristics compared to current events generated by the presence of Aβ1-42 in model membranes comprising a 1:1 mixture of DOPS and POPE lipids. Oligomers of the truncated Aβ fragment Aβ17-42 (p3) exhibited similar ion conductivity behavior as Aβ1-42 in BTLE membranes. However, the observed macroscopic ion flux across the BTLE membranes induced by Aβ1-42 pores was larger than for p3 pores. Our analysis of structure and conductance of oligomeric Aβ pores in a natural lipid membrane closely mimics the in vivo cellular environment suggesting that Aβ pores could potentially accelerate the loss of ionic homeostasis and cellular abnormalities. Hence, these pore structures may serve as a target for drug development and therapeutic strategies for AD treatment.
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Affiliation(s)
| | | | - Fernando T Arce
- Division of Translational and Regenerative Medicine, Department of Medicine, Department of Biomedical Engineering, University of Arizona , Tucson, Arizona 85721, United States
| | | | - Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California , Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
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23
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Korshavn KJ, Satriano C, Lin Y, Zhang R, Dulchavsky M, Bhunia A, Ivanova MI, Lee YH, La Rosa C, Lim MH, Ramamoorthy A. Reduced Lipid Bilayer Thickness Regulates the Aggregation and Cytotoxicity of Amyloid-β. J Biol Chem 2017; 292:4638-4650. [PMID: 28154182 DOI: 10.1074/jbc.m116.764092] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/31/2017] [Indexed: 11/06/2022] Open
Abstract
The aggregation of amyloid-β (Aβ) on lipid bilayers has been implicated as a mechanism by which Aβ exerts its toxicity in Alzheimer's disease (AD). Lipid bilayer thinning has been observed during both oxidative stress and protein aggregation in AD, but whether these pathological modifications of the bilayer correlate with Aβ misfolding is unclear. Here, we studied peptide-lipid interactions in synthetic bilayers of the short-chain lipid dilauroyl phosphatidylcholine (DLPC) as a simplified model for diseased bilayers to determine their impact on Aβ aggregate, protofibril, and fibril formation. Aβ aggregation and fibril formation in membranes composed of dioleoyl phosphatidylcholine (DOPC) or 1- palmitoyl-2-oleoyl phosphatidylcholine mimicking normal bilayers served as controls. Differences in aggregate formation and stability were monitored by a combination of thioflavin-T fluorescence, circular dichroism, atomic force microscopy, transmission electron microscopy, and NMR. Despite the ability of all three lipid bilayers to catalyze aggregation, DLPC accelerates aggregation at much lower concentrations and prevents the fibrillation of Aβ at low micromolar concentrations. DLPC stabilized globular, membrane-associated oligomers, which could disrupt the bilayer integrity. DLPC bilayers also remodeled preformed amyloid fibrils into a pseudo-unfolded, molten globule state, which resembled on-pathway, protofibrillar aggregates. Whereas the stabilized, membrane-associated oligomers were found to be nontoxic, the remodeled species displayed toxicity similar to that of conventionally prepared aggregates. These results provide mechanistic insights into the roles that pathologically thin bilayers may play in Aβ aggregation on neuronal bilayers, and pathological lipid oxidation may contribute to Aβ misfolding.
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Affiliation(s)
- Kyle J Korshavn
- From the Department of Chemistry.,Program in Biophysics, and
| | - Cristina Satriano
- the Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Yuxi Lin
- the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - Mark Dulchavsky
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Anirban Bhunia
- the Department of Biophysics, Bose Institute, Kolkata 700009, India, and
| | - Magdalena I Ivanova
- Program in Biophysics, and.,Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Young-Ho Lee
- the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Carmelo La Rosa
- the Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Mi Hee Lim
- the Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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24
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Gillman AL, Lee J, Ramachandran S, Capone R, Gonzalez T, Wrasidlo W, Masliah E, Lal R. Small molecule NPT-440-1 inhibits ionic flux through Aβ 1-42 pores: Implications for Alzheimer's disease therapeutics. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2016; 12:2331-2340. [PMID: 27335341 PMCID: PMC5116404 DOI: 10.1016/j.nano.2016.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/31/2016] [Accepted: 06/04/2016] [Indexed: 12/11/2022]
Abstract
Increased levels of soluble amyloid-beta (Aβ) oligomers are suspected to underlie Alzheimer's disease (AD) pathophysiology. These oligomers have been shown to form multi-subunit Aβ pores in bilayers and induce uncontrolled, neurotoxic, ion flux, particularly calcium ions, across cellular membranes that might underlie cognitive impairment in AD. Small molecule interventions that modulate pore activity could effectively prevent or ameliorate their toxic activity. Here we examined the efficacy of a small molecule, NPT-440-1, on modulating amyloid pore permeability. Co-incubation of B103 rat neuronal cells with NPT-440-1 and Aβ1-42 prevented calcium influx. In purified lipid bilayers, we show that a 10-15min preincubation, prior to membrane introduction, was required to prevent conductance. Thioflavin-T and circular dichroism both suggested a reduction in Aβ1-42 β-sheet content during this incubation period. Combined with previous studies on site-specific amino acid substitutions, these results suggest that pharmacological modulation of Aβ1-42 could prevent amyloid pore-mediated AD pathogenesis.
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Affiliation(s)
- Alan L Gillman
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
| | - Joon Lee
- Department of Mechanical and Aerospace Engineering University of California, San Diego, La Jolla, CA, United States
| | - Srinivasan Ramachandran
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States; Department of Mechanical and Aerospace Engineering University of California, San Diego, La Jolla, CA, United States
| | - Ricardo Capone
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Tania Gonzalez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
| | - Wolf Wrasidlo
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States; Neuropore Therapies, Inc., San Diego, CA, United States
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States.
| | - Ratnesh Lal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States; Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA, United States; Department of Mechanical and Aerospace Engineering University of California, San Diego, La Jolla, CA, United States.
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25
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Hecel A, De Ricco R, Valensin D. Influence of membrane environments and copper ions on the structural features of amyloidogenic proteins correlated to neurodegeneration. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Membrane binding of peptide models for early stages of amyloid formation: Lipid packing counts more than charge. Chem Phys Lipids 2016; 198:28-38. [DOI: 10.1016/j.chemphyslip.2016.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 02/04/2016] [Accepted: 02/27/2016] [Indexed: 11/17/2022]
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27
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Wineman-Fisher V, Miller Y. Structural Insights into the Polymorphism of Self-Assembled Amylin Oligomers. Isr J Chem 2016. [DOI: 10.1002/ijch.201500091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Vered Wineman-Fisher
- Department of Chemistry
- Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; 84105 Beer-Sheva Israel
| | - Yifat Miller
- Department of Chemistry
- Ilse Katz Institute for Nanoscale Science and Technology; Ben-Gurion University of the Negev; 84105 Beer-Sheva Israel
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28
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Jang H, Arce FT, Lee J, Gillman AL, Ramachandran S, Kagan BL, Lal R, Nussinov R. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels. Methods Mol Biol 2016; 1345:251-68. [PMID: 26453217 PMCID: PMC7511997 DOI: 10.1007/978-1-4939-2978-8_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Aggregation can be studied by a range of methods, experimental and computational. Aggregates form in solution, across solid surfaces, and on and in the membrane, where they may assemble into unregulated leaking ion channels. Experimental probes of ion channel conformations and dynamics are challenging. Atomistic molecular dynamics (MD) simulations are capable of providing insight into structural details of amyloid ion channels in the membrane at a resolution not achievable experimentally. Since data suggest that late stage Alzheimer's disease involves formation of toxic ion channels, MD simulations have been used aiming to gain insight into the channel shapes, morphologies, pore dimensions, conformational heterogeneity, and activity. These can be exploited for drug discovery. Here we describe computational methods to model amyloid ion channels containing the β-sheet motif at atomic scale and to calculate toxic pore activity in the membrane.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
| | - Fernando Teran Arce
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Joon Lee
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alan L Gillman
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bruce L Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90024, USA
| | - Ratnesh Lal
- Department of Bioengineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, Materials Science Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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29
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Yi X, Zhang Y, Gong M, Yu X, Darabedian N, Zheng J, Zhou F. Ca2+ Interacts with Glu-22 of Aβ(1–42) and Phospholipid Bilayers to Accelerate the Aβ(1–42) Aggregation Below the Critical Micelle Concentration. Biochemistry 2015; 54:6323-32. [DOI: 10.1021/acs.biochem.5b00719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xinyao Yi
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
- College
of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Yi Zhang
- College
of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Ming Gong
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
| | - Xiang Yu
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Narek Darabedian
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
| | - Jie Zheng
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Feimeng Zhou
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
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30
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Wang X, Weber JK, Liu L, Dong M, Zhou R, Li J. A novel form of β-strand assembly observed in Aβ(33-42) adsorbed onto graphene. NANOSCALE 2015; 7:15341-15348. [PMID: 26331805 DOI: 10.1039/c5nr00555h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Peptide assembly plays a seminal role in the fabrication of structural and functional architectures in cells. Characteristically, peptide assemblies are often dominated by β-sheet structures, wherein component molecules are connected by backbone hydrogen bonds in a parallel or an antiparallel fashion. While β-rich peptide scaffolds are implicated in an array of neurodegenerative diseases, the mechanisms by which toxic peptides assemble and mediate neuropathic effects are still poorly understood. In this work, we employ molecular dynamics simulations to study the adsorption and assembly of the fragment Aβ33-42 (taken from the Aβ-42 peptide widely associated with Alzheimer's disease) on a graphene surface. We observe that such Aβ33-42 fragments, which are largely hydrophobic in character, readily adsorb onto the graphitic surface and coalesce into a well-structured, β-strand-like assembly. Strikingly, the structure of such complex is quite unique: hydrophobic side-chains extend over the graphene surface and interact with adjacent peptides, yielding a well-defined mosaic of hydrophobic interaction patches. This ordered structure is markedly depleted of backbone hydrogen bonds. Hence, our simulation results reveal a distinct type of β-strand assembly, maintained by hydrophobic side-chain interactions. Our finding suggests the backbone hydrogen bond is no longer crucial to the peptide assembly. Further studies concerning whether such β-strand assembly can be realized in other peptide systems and in biologically-relevant contexts are certainly warranted.
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Affiliation(s)
- Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing 100049, China.
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31
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Anunciado D, Rai DK, Qian S, Urban V, O'Neill H. Small-angle neutron scattering reveals the assembly of alpha-synuclein in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1881-1889. [PMID: 26321599 DOI: 10.1016/j.bbapap.2015.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/12/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022]
Abstract
The aggregation of α-synuclein (asyn), an intrinsically disordered protein (IDP), is a hallmark in Parkinson's disease (PD). We investigated the conformational changes that asyn undergoes in the presence of membrane and membrane mimetics using small-angle neutron scattering (SANS). In solution, asyn is monomeric and unfolded assuming an ensemble of conformers spanning extended and compact conformations. Using the contrast variation technique and SANS, the protein scattering signal in the membrane-protein complexes is selectively highlighted in order to monitor its conformational changes in this environment. We showed that in the presence of phospholipid membranes asyn transitions from a monodisperse state to aggregated structures with sizes ranging from 200 to 900Å coexisting with the monomeric species. Detailed SANS data analysis revealed that asyn aggregates have a hierarchical organization in which clusters of smaller asyn aggregates assemble to form the larger structures. This study provides new insight into the mechanism of asyn aggregation. We propose an aggregation mechanism in which stable asyn aggregates seed the aggregation process and hence the hierarchical assembly of structures. Our findings demonstrate that membrane-induced conformational changes in asyn lead to its heterogeneous aggregation which could be physiologically relevant in its function or in the diseased state.
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Affiliation(s)
- Divina Anunciado
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Durgesh K Rai
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Shuo Qian
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Volker Urban
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
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32
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Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev 2014; 43:6750-64. [PMID: 24566672 PMCID: PMC4143503 DOI: 10.1039/c3cs60459d] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Aggregation of disordered amyloidogenic peptides into oligomers is the causative agent of amyloid-related diseases. In solution, disordered protein states are characterized by heterogeneous ensembles. Among these, β-rich conformers self-assemble via a conformational selection mechanism to form energetically-favored cross-β structures, regardless of their precise sequences. These disordered peptides can also penetrate the membrane, and electrophysiological data indicate that they form ion-conducting channels. Based on these and additional data, including imaging and molecular dynamics simulations of a range of amyloid peptides, Alzheimer's amyloid-β (Aβ) peptide, its disease-related variants with point mutations and N-terminal truncated species, other amyloidogenic peptides, as well as a cytolytic peptide and a synthetic gel-forming peptide, we suggest that disordered amyloidogenic peptides can also present a common motif in the membrane. The motif consists of curved, moon-like β-rich oligomers associated into annular organizations. The motif is favored in the lipid bilayer since it permits hydrophobic side chains to face and interact with the membrane and the charged/polar residues to face the solvated channel pores. Such channels are toxic since their pores allow uncontrolled leakage of ions into/out of the cell, destabilizing cellular ionic homeostasis. Here we detail Aβ, whose aggregation is associated with Alzheimer's disease (AD) and for which there are the most abundant data. AD is a protein misfolding disease characterized by a build-up of Aβ peptide as senile plaques, neurodegeneration, and memory loss. Excessively produced Aβ peptides may directly induce cellular toxicity, even without the involvement of membrane receptors through Aβ peptide-plasma membrane interactions.
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Affiliation(s)
- Hyunbum Jang
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, U.S.A
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, U.S.A
| | - Ruth Nussinov
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, U.S.A
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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33
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Poojari C, Xiao D, Batista VS, Strodel B. Membrane permeation induced by aggregates of human islet amyloid polypeptides. Biophys J 2014; 105:2323-32. [PMID: 24268144 DOI: 10.1016/j.bpj.2013.09.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 09/12/2013] [Accepted: 09/30/2013] [Indexed: 01/23/2023] Open
Abstract
Several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases as well as nonneuropathic diseases such as type II diabetes and atrial amyloidosis are associated with aggregation of amyloid polypeptides into fibrillar structures, or plaques. In this study, we use molecular dynamics simulations to test the stability and orientation of membrane-embedded aggregates of the human islet amyloid polypeptide (hIAPP) implicated in type II diabetes. We find that in both monolayers and bilayers of dipalmitoylphosphatidylglycerol (DPPG) hIAPP trimers and tetramers remain inside the membranes and preserve their β-sheet secondary structure. Lipid bilayer-inserted hIAPP trimers and tetramers orient inside DPPG at 60° relative to the membrane/water interface and lead to water permeation and Na(+) intrusion, consistent with ion-toxicity in islet β-cells. In particular, hIAPP trimers form a water-filled β-sandwich that induce water permeability comparable with channel-forming proteins, such as aquaporins and gramicidin-A. The predicted disruptive orientation is consistent with the amphiphilic properties of the hIAPP aggregates and could be probed by chiral sum frequency generation (SFG) spectroscopy, as predicted by the simulated SFG spectra.
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Affiliation(s)
- Chetan Poojari
- Forschungszentrum Jülich GmbH, Institute of Complex Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
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34
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Lee J, Gillman AL, Jang H, Ramachandran S, Kagan BL, Nussinov R, Teran Arce F. Role of the fast kinetics of pyroglutamate-modified amyloid-β oligomers in membrane binding and membrane permeability. Biochemistry 2014; 53:4704-14. [PMID: 24950761 PMCID: PMC4215883 DOI: 10.1021/bi500587p] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Membrane
permeability to ions and small molecules is believed to
be a critical step in the pathology of Alzheimer’s disease
(AD). Interactions of oligomers formed by amyloid-β (Aβ)
peptides with the plasma cell membrane are believed to play a fundamental
role in the processes leading to membrane permeability. Among the
family of Aβs, pyroglutamate (pE)-modified Aβ peptides
constitute the most abundant oligomeric species in the brains of AD
patients. Although membrane permeability mechanisms have been studied
for full-length Aβ1–40/42 peptides, these
have not been sufficiently characterized for the more abundant AβpE3–42 fragment. Here we have compared the adsorbed
and membrane-inserted oligomeric species of AβpE3–42 and Aβ1–42 peptides. We find lower concentrations
and larger dimensions for both species of membrane-associated AβpE3–42 oligomers. The larger dimensions are attributed
to the faster self-assembly kinetics of AβpE3–42, and the lower concentrations are attributed to weaker interactions
with zwitterionic lipid headgroups. While adsorbed oligomers produced
little or no significant membrane structural damage, increased membrane
permeabilization to ionic species is understood in terms of enlarged
membrane-inserted oligomers. Membrane-inserted AβpE3–42 oligomers were also found to modify the mechanical properties of
the membrane. Taken together, our results suggest that membrane-inserted
oligomers are the primary species responsible for membrane permeability.
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Affiliation(s)
- Joon Lee
- Department of Bioengineering, University of California at San Diego , La Jolla, California 92093, United States
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35
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Gillman AL, Jang H, Lee J, Ramachandran S, Kagan B, Nussinov R, Teran Arce F. Activity and architecture of pyroglutamate-modified amyloid-β (AβpE3-42) pores. J Phys Chem B 2014; 118:7335-44. [PMID: 24922585 PMCID: PMC4096221 DOI: 10.1021/jp5040954] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/10/2014] [Indexed: 12/17/2022]
Abstract
Among the family of Aβ peptides, pyroglutamate-modified Aβ (AβpE) peptides are particularly associated with cytotoxicity in Alzheimer's disease (AD). They represent the dominant fraction of Aβ oligomers in the brains of AD patients, but their accumulation in the brains of elderly individuals with normal cognition is significantly lower. Accumulation of AβpE plaques precedes the formation of plaques of full-length Aβ (Aβ1-40/42). Most of these properties appear to be associated with the higher hydrophobicity of AβpE as well as an increased resistance to enzymatic degradation. However, the important question of whether AβpE peptides induce pore activity in lipid membranes and their potential toxicity compared with other Aβ pores is still open. Here we examine the activity of AβpE pores in anionic membranes using planar bilayer electrical recording and provide their structures using molecular dynamics simulations. We find that AβpE pores spontaneously induce ionic current across the membrane and have some similar properties to the other previously studied pores of the Aβ family. However, there are also some significant differences. The onset of AβpE3-42 pore activity is generally delayed compared with Aβ1-42 pores. However, once formed, AβpE3-42 pores produce increased ion permeability of the membrane, as indicated by a greater occurrence of higher conductance electrical events. Structurally, the lactam ring of AβpE peptides induces a change in the conformation of the N-terminal strands of the AβpE3-42 pores. While the N-termini of wild-type Aβ1-42 peptides normally reside in the bulk water region, the N-termini of AβpE3-42 peptides tend to reside in the hydrophobic lipid core. These studies provide a first step to an understanding of the enhanced toxicity attributed to AβpE peptides.
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Affiliation(s)
- Alan L. Gillman
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
| | - Hyunbum Jang
- Cancer
and Inflammation Program, National Cancer Institute at Frederick,
Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Joon Lee
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Srinivasan Ramachandran
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Bruce
L. Kagan
- Department
of Psychiatry, David Geffen School of Medicine, Semel Institute for
Neuroscience and Human Behavior, University
of California, 760 Westwood
Plaza, Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Cancer
and Inflammation Program, National Cancer Institute at Frederick,
Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department
of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Fernando Teran Arce
- Department
of Bioengineering, University of California,
San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
- Department
of Mechanical and Aerospace Engineering and Material Science Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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36
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Li Q, Liu L, Zhang S, Xu M, Wang X, Wang C, Besenbacher F, Dong M. Modulating aβ33-42 peptide assembly by graphene oxide. Chemistry 2014; 20:7236-40. [PMID: 24838837 DOI: 10.1002/chem.201402022] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Indexed: 12/12/2022]
Abstract
Graphene oxide (GO) is utilized as the modulator to tune the formation and development of amyloid fibrils (Aβ33-42 ). Atomic force microscopy temporal evolution measurements reveal that the initial binding between the peptide monomer and the large available surface of the GO sheets can redirect the assembly pathway of amyloid beta. The results support the possibility to develop graphene-based materials to inhibit amyloidosis.
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Affiliation(s)
- Qiang Li
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C (Denmark), Fax: (+45) 8942-3690
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37
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Morriss-Andrews A, Brown FLH, Shea JE. A coarse-grained model for peptide aggregation on a membrane surface. J Phys Chem B 2014; 118:8420-32. [PMID: 24791936 DOI: 10.1021/jp502871m] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aggregation of peptides on a lipid bilayer is studied using coarse-grained molecular dynamics in implicit solvent. Peptides bind to and self-assemble on the membrane surface into β-rich fibrillar aggregates, even under conditions where only disordered oligomers form in bulk solution. Relative to a solid surface, the membrane surface facilitates peptide mobility and a more complex network of morphology transitions as aggregation proceeds. Additionally, final aggregate structures realized on the membrane surface are distinct from those observed on a comparable solid surface. The aggregated fibrils alter the local structure and material properties of the lipid bilayer in their immediate vicinity but have only a modest effect on the overall bending rigidity of the bilayer.
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Affiliation(s)
- Alex Morriss-Andrews
- Department of Physics, University of California Santa Barbara , Santa Barbara, California 93106, United States
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38
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Probing the interplay between amyloidogenic proteins and membranes using lipid monolayers and bilayers. Adv Colloid Interface Sci 2014; 207:81-92. [PMID: 24200086 DOI: 10.1016/j.cis.2013.10.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/11/2013] [Accepted: 10/13/2013] [Indexed: 11/21/2022]
Abstract
Many degenerative diseases such as Alzheimer's and Parkinson's involve proteins that have a tendency to misfold and aggregate eventually forming amyloid fibers. This review describes the use of monolayers, bilayers, supported membranes, and vesicles as model systems that have helped elucidate the mechanisms and consequences of the interactions between amyloidogenic proteins and membranes. These are twofold: membranes favor the formation of amyloid structures and these induce damage in those membranes. We describe studies that show how interfaces, especially charged ones, favor amyloidogenic protein aggregation by several means. First, surfaces increase the effective protein concentration reducing a three-dimensional system to a two-dimensional one. Second, charged surfaces allow electrostatic interactions with the protein. Anionic lipids as well as rafts, rich in cholesterol and gangliosides, prove to play an especially important role. Finally, these amphipathic systems also offer a hydrophobic environment favoring conformational changes, oligomerization, and eventual formation of mature fibers. In addition, we examine several models for membrane permeabilization: protein pores, leakage induced by extraction of lipids, chaotic pores, and membrane tension, presenting illustrative examples of experimental evidence in support of these models. The picture that emerges from recent work is one where more than one mechanism is in play. Which mechanism prevails depends on the protein, its aggregation state, and the lipid environment in which the interactions occur.
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39
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Bucciantini M, Rigacci S, Stefani M. Amyloid Aggregation: Role of Biological Membranes and the Aggregate-Membrane System. J Phys Chem Lett 2014; 5:517-27. [PMID: 26276603 DOI: 10.1021/jz4024354] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Several human degenerative diseases involve amyloidogenic peptides/proteins with high conformational plasticity and propensity to self-aggregate into polymeric fibrillar assemblies sharing the cross-β structure and endowed with cytotoxic potential. Although the mechanisms of amyloid growth and toxicity are not fully understood, a common property of amyloids is their ability to interact with lipid bilayers disturbing membrane integrity. Lipid bilayers can also act as conformational catalysts, favoring protein misfolding and inducing the growth of aggregation nuclei, early oligomers, and mature fibrils with specific biophysical, structural, and toxicity features. This Perspective will highlight these effects in the context of a membrane-oligomer system where the conformational/biophysical features of either component affect those of the other. In this context, we will highlight the modulation of the protein-cell surface interaction by the content of membrane cholesterol and gangliosides, notably GM1. In particular, we will discuss data that indicate how these interactions affect the structural and stability properties of both protein and bilayers as well as the final cytotoxic effect. Our goal is to propose shared membrane-based mechanisms that could apply to any amyloidogenic peptide/protein, providing a biochemical background for amyloid growth and toxicity.
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Affiliation(s)
- Monica Bucciantini
- †Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, V.le Morgagni 50, 50134 Florence, Italy
| | - Stefania Rigacci
- †Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, V.le Morgagni 50, 50134 Florence, Italy
| | - Massimo Stefani
- †Department of Biomedical Experimental and Clinical Sciences and Research Centre on the Molecular Basis of Neurodegeneration, University of Florence, V.le Morgagni 50, 50134 Florence, Italy
- ‡National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome, Italy
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Jana AK, Sengupta N. Surface induced collapse of Aβ1-42 with the F19A replacement following adsorption on a single walled carbon nanotube. Biophys Chem 2013; 184:108-15. [DOI: 10.1016/j.bpc.2013.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/25/2013] [Accepted: 09/28/2013] [Indexed: 12/12/2022]
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Poojari C, Strodel B. Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations. PLoS One 2013; 8:e78399. [PMID: 24244308 PMCID: PMC3820573 DOI: 10.1371/journal.pone.0078399] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022] Open
Abstract
Interactions of the amyloid β-protein (Aβ) with neuronal cell membranes, leading to the disruption of membrane integrity, are considered to play a key role in the development of Alzheimer’s disease. Natural mutations in Aβ42, such as the Arctic mutation (E22G) have been shown to increase Aβ42 aggregation and neurotoxicity, leading to the early-onset of Alzheimer’s disease. A correlation between the propensity of Aβ42 to form protofibrils and its effect on neuronal dysfunction and degeneration has been established. Using rational mutagenesis of the Aβ42 peptide it was further revealed that the aggregation of different Aβ42 mutants in lipid membranes results in a variety of polymorphic aggregates in a mutation dependent manner. The mutant peptides also have a variable ability to disrupt bilayer integrity. To further test the connection between Aβ42 mutation and peptide–membrane interactions, we perform molecular dynamics simulations of membrane-inserted Aβ42 variants (wild-type and E22G, D23G, E22G/D23G, K16M/K28M and K16M/E22G/D23G/K28M mutants) as β-sheet monomers and tetramers. The effects of charged residues on transmembrane Aβ42 stability and membrane integrity are analyzed at atomistic level. We observe an increased stability for the E22G Aβ42 peptide and a decreased stability for D23G compared to wild-type Aβ42, while D23G has the largest membrane-disruptive effect. These results support the experimental observation that the altered toxicity arising from mutations in Aβ is not only a result of the altered aggregation propensity, but also originates from modified Aβ interactions with neuronal membranes.
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Affiliation(s)
- Chetan Poojari
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- * E-mail:
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42
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Interactions between Aβ and mutated Tau lead to polymorphism and induce aggregation of Aβ-mutated tau oligomeric complexes. PLoS One 2013; 8:e73303. [PMID: 23951348 PMCID: PMC3741189 DOI: 10.1371/journal.pone.0073303] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/18/2013] [Indexed: 11/19/2022] Open
Abstract
One of the main hallmarks of the fronto-temporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17) is the accumulation of neurofibrillary tangles in the brain as an outcome of the aggregation of mutated tau protein. This process occurs due to a number of genetic mutations in the MAPT gene. One of these mutations is the ∆K280 mutation in the tau R2 repeat domain, which promotes the aggregation vis-à-vis that for the wild-type tau. Experimental studies have shown that in Alzheimer's disease Aβ peptide forms aggregates both with itself and with wild-type tau. By analogy, in FTDP-17, it is likely that there are interactions between Aβ and mutated tau, but the molecular mechanisms underlying such interactions remain to be elucidated. Thus, to investigate the interactions between Aβ and mutated tau, we constructed fourteen ∆K280 mutated tau-Aβ17-42 oligomeric complexes. In seven of the mutated tau-Aβ17-42 oligoemric complexes the mutated tau oligomers exhibited hydrophobic interactions in their core domain, and in the other seven mutated tau-Aβ17-42 oligoemric complexes the mutated tau oligomers exhibited salt-bridge interactions in their core domain. We considered two types of interactions between mutated tau oligomers and Aβ oligomers: interactions of one monomer of the Aβ oligomer with one monomer of the mutated tau oligomer to form a single-layer conformation, and interactions of the entire Aβ oligomer with the entire mutated tau oligomer to form a double-layer conformation. We also considered parallel arrangements of Aβ trimers alternating with mutated tau trimers in a single-layer conformation. Our results demonstrate that in the interactions of Aβ and mutated tau oligomers, polymorphic mutated tau-Aβ17-42 oligomeric complexes were observed, with a slight preference for the double-layer conformation. Aβ trimers alternating with mutated tau trimers constituted a structurally stable confined β-structure, albeit one that was energetically less stable than all the other constructed models.
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Li C, Mezzenga R. The interplay between carbon nanomaterials and amyloid fibrils in bio-nanotechnology. NANOSCALE 2013; 5:6207-6218. [PMID: 23744243 DOI: 10.1039/c3nr01644g] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent advances in bio-nanotechnology have not only rapidly broadened the applications and scope of hybrid nanomaterials in biological fields, but also greatly enriched the examples of ordered materials based on supramolecular self-assembly. Among eminent examples of functional nanostructured materials of undisputed impact in nanotechnology and biological environments, carbon nanomaterials (such as fullerenes, carbon nanotubes and graphene) and amyloid fibrils have attracted great attention because of their unique architectures and exceptional physical properties. Nonetheless, combination of these two classes of nanomaterials into functional hybrids is far from trivial. For example, the presence of carbon nanomaterials can offer either an inhibitory effect or promotion of amyloid fibrillation, depending on the structural architectures of carbon nanomaterials and the starting amyloid proteins/peptides considered. To date, numerous studies have been devoted to evaluating both the biological toxicity of carbon nanomaterials and their use in developing therapies for amyloidosis. At the same time, hybridization of these two classes of nanomaterials offers new possibilities for combining some of their desirable properties into nanocomposites of possible use in electronics, actuators, sensing, biomedicine and structural materials. This review describes recent developments in the hybridization of carbon nanomaterials and amyloid fibrils and discusses the current state of the art on the application of carbon nanomaterial-amyloid fibril hybrids in bio-nanotechnology.
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Affiliation(s)
- Chaoxu Li
- ETH Zurich, Food & Soft Materials, Department of Health Science & Technology, Zurich, Switzerland
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Jose JC, Sengupta N. Molecular dynamics simulation studies of the structural response of an isolated Aβ1–42 monomer localized in the vicinity of the hydrophilic TiO2 surface. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:487-94. [DOI: 10.1007/s00249-013-0900-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/21/2013] [Accepted: 03/21/2013] [Indexed: 12/12/2022]
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Yu X, Wang Q, Pan Q, Zhou F, Zheng J. Molecular interactions of Alzheimer amyloid-β oligomers with neutral and negatively charged lipid bilayers. Phys Chem Chem Phys 2013; 15:8878-89. [PMID: 23493873 DOI: 10.1039/c3cp44448a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Interaction of p3 (Aβ(17-42)) peptides with cell membranes is crucial for the understanding of amyloid toxicity associated with Alzheimer's disease (AD). Such p3-membrane interactions are considered to induce the disruption of membrane permeability and integrity, but the exact mechanisms of how p3 aggregates, particularly small p3 oligomers, induce receptor-independent membrane disruption are not yet completely understood. Here, we investigate the adsorption, orientation, and surface interaction of the p3 pentamer with lipid bilayers composed of both pure zwitterionic POPC (palmitoyl-oleoyl-phosphatidylcholine) and mixed anionic POPC-POPG (palmitoyl-oleoyl-phosphatidylglycerol) (3 : 1) lipids using explicit-solvent molecular dynamics (MD) simulations. MD simulation results show that the p3 pentamer has much stronger interactions with mixed POPC-POPG lipids than pure POPC lipids, consistent with experimental observation that Aβ adsorption and fibrillation are enhanced on anionic lipid bilayers. Although electrostatic interactions are main attractive forces to drive the p3 pentamer to adsorb on the bilayer surface, the adsorption of the p3 pentamer on the lipid bilayer with C-terminal β-strands facing toward the bilayer surface is a net outcome of different competitions between p3 peptides-lipid bilayer and ions-p3-bilayer interactions. More importantly, Ca(2+) ions are found to form ionic bridges to associate negatively charged residues of p3 with anionic headgroups of the lipid bilayer, resulting in Aβ-Ca(2+)-PO4(-) complexes. Intensive Ca(2+) bound to the lipid bilayer and Ca(2+) ionic bridges may lead to Ca(2+) hemostasis responsible for neuronal dysfunction and death. This work provides insights into the mutual structure, dynamics, and interactions of both Aβ peptides and lipid bilayers at the atomic level, which expand our understanding of the complex behavior of amyloid-induced membrane disruption.
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Affiliation(s)
- Xiang Yu
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, USA
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Li JJ, Yip CM. Super-resolved FT-IR spectroscopy: Strategies, challenges, and opportunities for membrane biophysics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2272-82. [PMID: 23500349 DOI: 10.1016/j.bbamem.2013.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 02/25/2013] [Indexed: 01/16/2023]
Abstract
Direct correlation of molecular conformation with local structure is critical to studies of protein- and peptide-membrane interactions, particularly in the context of membrane-facilitated aggregation, and disruption or disordering. Infrared spectroscopy has long been a mainstay for determining molecular conformation, following folding dynamics, and characterizing reactions. While tremendous advances have been made in improving the spectral and temporal resolution of infrared spectroscopy, it has only been with the introduction of scanned-probe techniques that exploit the raster-scanning tip as either a source, scattering tool, or measurement probe that researchers have been able to obtain sub-diffraction limit IR spectra. This review will examine the history of correlated scanned-probe IR spectroscopies, from their inception to their use in studies of molecular aggregates, membrane domains, and cellular structures. The challenges and opportunities that these platforms present for examining dynamic phenomena will be discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Jessica J Li
- Department of Chemical Engineering and Applied Chemistry, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada M5S 3E1
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Poojari C, Kukol A, Strodel B. How the amyloid-β peptide and membranes affect each other: An extensive simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:327-39. [DOI: 10.1016/j.bbamem.2012.09.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/24/2022]
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Jang H, Connelly L, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane. J Chem Theory Comput 2013; 9:822-833. [PMID: 23316126 PMCID: PMC3539805 DOI: 10.1021/ct300916f] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid-β (Aβ) oligomers destabilize cellular ionic homeostasis, mediating Alzheimer's disease (AD). It is still unclear whether the mechanism (i) is mediated by cell surface receptors; (ii) is direct, with Aβ oligomers interacting with membrane lipids; or (iii) both mechanisms take place. Recent studies indicate that Aβ oligomers may act by either of the last two. Little is known about the oligomers' structures and how they spontaneously insert into the membrane. Using explicit solvent molecular dynamics (MD) simulations, we show that fibril-like Aβ(17-42) (p3) oligomer is capable of penetrating the membrane. Insertion is similar to that observed for protegrin-1 (PG-1), a cytolytic β-sheet-rich antimicrobial peptide (AMP). Both Aβ and PG-1 favor the amphipathic interface of the lipid bilayer in the early stage of interaction with the membrane. U-shaped Aβ oligomers are observed in solution and in the membrane, suggesting that the preformed seeds can be shared by amyloid fibrils in the growth phase and membrane toxicity. Here we provide sequential events in possible Aβ oligomer membrane-insertion pathways. We speculate that for the U-shaped motif, a trimer is the minimal oligomer size to insert effectively. We propose that monomers and dimers may insert in (apparently on-pathway) aggregation-intermediate β-hairpin state, and may (or may not) convert to a U-shape in the bilayer. Together with earlier observations, our results point to a non-specific, broadly heterogeneous landscape of membrane-inserting oligomer conformations, pathways, and membrane-mediated toxicity of β-rich oligomers.
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Affiliation(s)
- Hyunbum Jang
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Laura Connelly
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Fernando Teran Arce
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Bruce L. Kagan
- Department of Psychiatry, David Geffen School of Medicine, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90024, USA
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering, and Materials Science Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Afrasiabi R, Kraatz HB. Sonication-Induced Coiled Fibrous Architectures of Boc-L-Phe-L-Lys(Z)-OMe. Chemistry 2012; 19:1769-77. [DOI: 10.1002/chem.201202268] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/27/2012] [Indexed: 12/29/2022]
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50
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Structural features and cytotoxicity of amyloid oligomers: Implications in Alzheimer's disease and other diseases with amyloid deposits. Prog Neurobiol 2012; 99:226-45. [DOI: 10.1016/j.pneurobio.2012.03.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 12/22/2022]
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