1
|
Karkisaval AG, Hassan R, Nguyen A, Balster B, Abedin F, Lal R, Tatulian SA. The structure of tyrosine-10 favors ionic conductance of Alzheimer's disease-associated full-length amyloid-β channels. Nat Commun 2024; 15:1296. [PMID: 38351257 PMCID: PMC10864385 DOI: 10.1038/s41467-023-43821-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/21/2023] [Indexed: 02/16/2024] Open
Abstract
Amyloid β (Aβ) ion channels destabilize cellular ionic homeostasis, which contributes to neurotoxicity in Alzheimer's disease. The relative roles of various Aβ isoforms are poorly understood. We use bilayer electrophysiology, AFM imaging, circular dichroism, FTIR and fluorescence spectroscopy to characterize channel activities of four most prevalent Aβ peptides, Aβ1-42, Aβ1-40, and their pyroglutamylated forms (AβpE3-42, AβpE3-40) and correlate them with the peptides' structural features. Solvent-induced fluorescence splitting of tyrosine-10 is discovered and used to assess the sequestration from the solvent and membrane insertion. Aβ1-42 effectively embeds in lipid membranes, contains large fraction of β-sheet in a β-barrel-like structure, forms multi-subunit pores in membranes, and displays well-defined ion channel features. In contrast, the other peptides are partially solvent-exposed, contain minimal β-sheet structure, form less-ordered assemblies, and produce irregular ionic currents. These findings illuminate the structural basis of Aβ neurotoxicity through membrane permeabilization and may help develop therapies that target Aβ-membrane interactions.
Collapse
Affiliation(s)
- Abhijith G Karkisaval
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rowan Hassan
- Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Andrew Nguyen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Balster
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Faisal Abedin
- Department of Physics, University of Central Florida, Orlando, FL, USA
- Department of Biology, Xavier University of Louisiana, New Orleans, LA, USA
| | - Ratnesh Lal
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL, USA.
| |
Collapse
|
2
|
Wang K, Cai W. Aggregation, structure and water permeability of membrane-embedded helical Aβ oligomers. Phys Chem Chem Phys 2024; 26:5128-5140. [PMID: 38259193 DOI: 10.1039/d3cp05317b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
It is widely recognized that membranes can facilitate the aggregation of amyloid-β (Aβ) peptides, while Aβ can in turn cause membrane damage. Many studies focus on the peptide-membrane interactions of Aβ oligomers with β-rich structures. However, the exact aggregation and toxicity mechanism of the membrane-embedded helical Aβ oligomers remain ambiguous. Herein, the molecular dynamics simulations were performed on membrane-embedded helical Aβ42 peptides. Initiated by eight Aβ42 monomers embedded in a lipid bilayer, the monomers aggregate into oligomers with stable transmembrane helix structures. With the aggregation of peptides, the membrane perturbations caused by Aβ aggregates decrease. The molecular architectures of oligomers were characterized and a helix-rich octamer stabilized by an annular network of hydrogen bonds was observed. The oligomers demonstrate the capability to assist transmembrane water transport. Our study may provide new insights for the investigation of transmembrane Aβ oligomers.
Collapse
Affiliation(s)
- Ke Wang
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Abstract
Perturbation of cell membranes by amyloid β (Ab) peptide oligomers is one possible mechanism of cytotoxicity in Alzheimer's disease, but the structure of such Ab-membrane complexes is unknown. Here we examine the stability of several putative structures by implicit membrane and all-atom molecular dynamics simulations. The structures include (a) a variety of models proposed by other researchers in the past, (b) a heptameric β barrel determined by grafting the Ab sequence onto α-hemolysin, (c) a similar structure with modified strand orientation and turn location based on an experimental β-hairpin structure, (d) oligomers inserting C-terminal β hairpins into one leaflet of the bilayer, (e) oligomers forming parallel C-terminal β barrels, and (f) a helical hexamer made of C-terminal fragments. The α-hemolysin-grafted structure and its alternately oriented variant are stable in the membrane and form an aqueous pore. In contrast, the C-terminal parallel barrels are not stable, presumably due to excessive hydrophobicity of their inner surface. The helical hexamer also failed to stabilize an aqueous pore for the same reason. The C-terminal hairpin-inserting structures remain stably inserted but, again, do not form an aqueous pore. Our results suggest that only β-barrels inserting a combination of C-terminal and other residues can form stable aqueous pores.
Collapse
Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York10016, United States
| |
Collapse
|
5
|
Krasnobaev VD, Batishchev OV. The Role of Lipid Domains and Physical Properties of Membranes in the Development of Age-Related Neurodegenerative Diseases. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s199074782209001x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
6
|
Trumbore CN, Raghunandan A. An Alzheimer's Disease Mechanism Based on Early Pathology, Anatomy, Vascular-Induced Flow, and Migration of Maximum Flow Stress Energy Location with Increasing Vascular Disease. J Alzheimers Dis 2022; 90:33-59. [PMID: 36155517 DOI: 10.3233/jad-220622] [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: 11/15/2022]
Abstract
This paper suggests a chemical mechanism for the earliest stages of Alzheimer's disease (AD). Cerebrospinal fluid (CSF) flow stresses provide the energy needed to induce molecular conformation changes leading to AD by initiating amyloid-β (Aβ) and tau aggregation. Shear and extensional flow stresses initiate aggregation in the laboratory and in natural biophysical processes. Energy-rich CSF flow regions are mainly found in lower brain regions. MRI studies reveal flow stress "hot spots" in basal cisterns and brain ventricles that have chaotic flow properties that can distort molecules such as Aβ and tau trapped in these regions into unusual conformations. Such fluid disturbance is surrounded by tissue deformation. There is strong mapping overlap between the locations of these hot spots and of early-stage AD pathology. Our mechanism creates pure and mixed protein dimers, followed by tissue surface adsorption, and long-term tissue agitation ultimately inducing chemical reactions forming more stable, toxic oligomer seeds that initiate AD. It is proposed that different flow stress energies and flow types in different basal brain regions produce different neurotoxic aggregates. Proliferating artery hardening is responsible for enhanced heart systolic pulses that drive energetic CSF pulses, whose critical maximum systolic pulse energy location migrates further from the heart with increasing vascular disease. Two glymphatic systems, carotid and basilar, are suggested to contain the earliest Aβ and tau AD disease pathologies. A key to the proposed AD mechanism is a comparison of early chronic traumatic encephalopathy and AD pathologies. Experiments that test the proposed mechanism are needed.
Collapse
Affiliation(s)
- Conrad N Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Aditya Raghunandan
- Department of Mechanical Engineering, University of Rochester, Rochester, NY, USA
| |
Collapse
|
7
|
Durell SR, Kayed R, Guy HR. The amyloid concentric β‐barrel hypothesis: Models of amyloid beta 42 oligomers and annular protofibrils. Proteins 2022; 90:1190-1209. [DOI: 10.1002/prot.26301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Stewart R. Durell
- Laboratory of Cell Biology, National Cancer Institute National Institutes of Health Bethesda Maryland USA
| | - Rakez Kayed
- UTMB Mitchell Center for Neurodegenerative Diseases, Department of Neurology University of Texas Medical Branch Galveston Texas USA
| | - H. Robert Guy
- Amyloid Research Consultants (ARC) Cochiti Lake New Mexico USA
| |
Collapse
|
8
|
Durell SR, Guy HR. The amyloid concentric β-barrel hypothesis: Models of synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels. Proteins 2022; 90:512-542. [PMID: 34570382 PMCID: PMC8988847 DOI: 10.1002/prot.26249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/13/2021] [Indexed: 02/03/2023]
Abstract
Amyloid beta (Aβ of Alzheimer's disease) and α-synuclein (α-Syn of Parkinson's disease) form large fibrils. Evidence is increasing however that much smaller oligomers are more toxic and that these oligomers can form transmembrane ion channels. We have proposed previously that Aβ42 oligomers, annular protofibrils, and ion channels adopt concentric β-barrel molecular structures. Here we extend that hypothesis to the superfamily of α, β, and γ-synucleins. Our models of numerous synuclein oligomers, annular protofibrils, tubular protofibrils, lipoproteins, and ion channels were developed to be consistent with sizes, shapes, molecular weights, and secondary structures of assemblies as determined by electron microscopy and other studies. The models have the following features: (1) all subunits have identical structures and interactions; (2) they are consistent with conventional β-barrel theory; (3) the distance between walls of adjacent β-barrels is between 0.6 and 1.2 nm; (4) hydrogen bonds, salt bridges, interactions among aromatic side-chains, burial and tight packing of hydrophobic side-chains, and aqueous solvent exposure of hydrophilic side-chains are relatively optimal; and (5) residues that are identical among distantly related homologous proteins cluster in the interior of most oligomers whereas residues that are hypervariable are exposed on protein surfaces. Atomic scale models of some assemblies were developed.
Collapse
Affiliation(s)
- Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - H Robert Guy
- Amyloid Research Consultants (ARC), Cochiti Lake, New Mexico, USA
| |
Collapse
|
9
|
Urban AS, Bershatskii YV, Pavlov KV, Bocharov EV. Structural Study of Membrane Glycoprotein-Precursor of β-Amyloid and Proteins Involved in Its Proteolysis. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Structural Studies Providing Insights into Production and Conformational Behavior of Amyloid-β Peptide Associated with Alzheimer's Disease Development. MOLECULES (BASEL, SWITZERLAND) 2021; 26:molecules26102897. [PMID: 34068293 PMCID: PMC8153327 DOI: 10.3390/molecules26102897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease is the most common type of neurodegenerative disease in the world. Genetic evidence strongly suggests that aberrant generation, aggregation, and/or clearance of neurotoxic amyloid-β peptides (Aβ) triggers the disease. Aβ accumulates at the points of contact of neurons in ordered cords and fibrils, forming the so-called senile plaques. Aβ isoforms of different lengths are found in healthy human brains regardless of age and appear to play a role in signaling pathways in the brain and to have neuroprotective properties at low concentrations. In recent years, different substances have been developed targeting Aβ production, aggregation, interaction with other molecules, and clearance, including peptide-based drugs. Aβ is a product of sequential cleavage of the membrane glycoprotein APP (amyloid precursor protein) by β- and γ-secretases. A number of familial mutations causing an early onset of the disease have been identified in the APP, especially in its transmembrane domain. The mutations are reported to influence the production, oligomerization, and conformational behavior of Aβ peptides. This review highlights the results of structural studies of the main proteins involved in Alzheimer's disease pathogenesis and the molecular mechanisms by which perspective therapeutic substances can affect Aβ production and nucleation.
Collapse
|
11
|
Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 378] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
Collapse
Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| |
Collapse
|
12
|
Trumbore CN. Shear-Induced Amyloid Aggregation in the Brain: V. Are Alzheimer's and Other Amyloid Diseases Initiated in the Lower Brain and Brainstem by Cerebrospinal Fluid Flow Stresses? J Alzheimers Dis 2021; 79:979-1002. [PMID: 33386802 PMCID: PMC7990457 DOI: 10.3233/jad-201025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Amyloid-β (Aβ) and tau oligomers have been identified as neurotoxic agents responsible for causing Alzheimer's disease (AD). Clinical trials using Aβ and tau as targets have failed, giving rise to calls for new research approaches to combat AD. This paper provides such an approach. Most basic AD research has involved quiescent Aβ and tau solutions. However, studies involving laminar and extensional flow of proteins have demonstrated that mechanical agitation of proteins induces or accelerates protein aggregation. Recent MRI brain studies have revealed high energy, chaotic motion of cerebrospinal fluid (CSF) in lower brain and brainstem regions. These and studies showing CSF flow within the brain have shown that there are two energetic hot spots. These are within the third and fourth brain ventricles and in the neighborhood of the circle of Willis blood vessel region. These two regions are also the same locations as those of the earliest Aβ and tau AD pathology. In this paper, it is proposed that cardiac systolic pulse waves that emanate from the major brain arteries in the lower brain and brainstem regions and whose pulse waves drive CSF flows within the brain are responsible for initiating AD and possibly other amyloid diseases. It is further proposed that the triggering of these diseases comes about because of the strengthening of systolic pulses due to major artery hardening that generates intense CSF extensional flow stress. Such stress provides the activation energy needed to induce conformational changes of both Aβ and tau within the lower brain and brainstem region, producing unique neurotoxic oligomer molecule conformations that induce AD.
Collapse
Affiliation(s)
- Conrad N. Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| |
Collapse
|
13
|
Fantini J, Chahinian H, Yahi N. Progress toward Alzheimer's disease treatment: Leveraging the Achilles' heel of Aβ oligomers? Protein Sci 2020; 29:1748-1759. [PMID: 32567070 DOI: 10.1002/pro.3906] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022]
Abstract
After three decades of false hopes and failures, a pipeline of therapeutic drugs that target the actual root cause of Alzheimer's disease (AD) is now available. Challenging the old paradigm that focused on β-amyloid peptide (Aβ) aggregation in amyloid plaques, these compounds are designed to prevent the neurotoxicity of Aβ oligomers that form Ca2+ permeable pores in the membranes of brain cells. By triggering an intracellular Ca2+ overdose, Aβ oligomers induce a cascade of neurotoxic events including oxidative stress, tau hyperphosphorylation, and neuronal loss. Targeting any post-Ca2+ entry steps (e.g., tau) will not address the root cause of the disease. Thus, preventing Aβ oligomers formation and/or blocking their toxicity is by essence the best approach to stop any progression of AD. Three categories of anti-oligomer compounds are already available: antibodies, synthetic peptides, and small drugs. Independent in silico-based designs of a peptide (AmyP53) and a monoclonal antibody (PMN310) converged to identify a histidine motif (H13/H14) that is critical for oligomer neutralization. This "histidine trick" can be viewed as the Achilles' heel of Aβ in the fight against AD. Moreover, lipid rafts and especially gangliosides play a critical role in the formation and toxicity of Aβ oligomers. Recognizing AD as a membrane disorder and gangliosides as the key anti-oligomer targets will provide innovative opportunities to find an efficient cure. A "full efficient" solution would also need to be affordable to anyone, as the number of patients has been following an exponential increase, affecting every part of the globe.
Collapse
Affiliation(s)
- Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Henri Chahinian
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Nouara Yahi
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| |
Collapse
|
14
|
Diociaiuti M, Bombelli C, Zanetti-Polzi L, Belfiore M, Fioravanti R, Macchia G, Giordani C. The Interaction between Amyloid Prefibrillar Oligomers of Salmon Calcitonin and a Lipid-Raft Model: Molecular Mechanisms Leading to Membrane Damage, Ca 2+-Influx and Neurotoxicity. Biomolecules 2019; 10:biom10010058. [PMID: 31905804 PMCID: PMC7022306 DOI: 10.3390/biom10010058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/19/2019] [Accepted: 12/27/2019] [Indexed: 12/14/2022] Open
Abstract
To investigate the interaction between amyloid assemblies and “lipid-rafts”, we performed functional and structural experiments on salmon calcitonin (sCT) solutions rich in prefibrillar oligomers, proto- and mature-fibers interacting with liposomes made of monosialoganglioside-GM1 (4%), DPPC (48%) and cholesterol (48%). To focus on the role played by electrostatic forces and considering that sCT is positive and GM1 is negative at physiologic pH, we compared results with those relative to GM1-free liposomes while, to assess membrane fluidity effects, with those relative to cholesterol-free liposomes. We investigated functional effects by evaluating Ca2+-influx in liposomes and viability of HT22-DIFF neurons. Only neurotoxic solutions rich in unstructured prefibrillar oligomers were able to induce Ca2+-influx in the “lipid-rafts” model, suggesting that the two phenomena were correlated. Thus, we investigated protein conformation and membrane modifications occurring during the interaction: circular dichroism showed that “lipid-rafts” fostered the formation of β-structures and energy filtered-transmission electron microscopy that prefibrillar oligomers formed pores, similar to Aβ did. We speculate that electrostatic forces between the positive prefibrillar oligomers and the negative GM1 drive the initial binding while the hydrophobic profile and flexibility of prefibrillar oligomers, together with the membrane fluidity, are responsible for the subsequent pore formation leading to Ca2+-influx and neurotoxicity.
Collapse
Affiliation(s)
- Marco Diociaiuti
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, I-00161 Roma, Italy; (M.B.); (R.F.)
- Correspondence: ; Tel.: +39-06-49902981
| | - Cecilia Bombelli
- CNR-Istituto per i Sistemi Biologici, UOS di Roma, c/o Dipartimento di Chimica, Sapienza Università di Roma, I-00185 Roma, Italy;
| | - Laura Zanetti-Polzi
- Dipartimento di Fisica e Scienze Chimiche, Università dell’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy;
| | - Marcello Belfiore
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, I-00161 Roma, Italy; (M.B.); (R.F.)
| | - Raoul Fioravanti
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, I-00161 Roma, Italy; (M.B.); (R.F.)
- Dipartimento di Chimica, Sapienza Università di Roma, I-00185 Roma, Italy
| | - Gianfranco Macchia
- Centro Grandi Strumentazioni e Core Facilities, Istituto Superiore di Sanità, I-00161 Roma, Italy;
| | - Cristiano Giordani
- Grupo Productos Naturales Marinos, Facultad de Ciencias Farmacéuticas y Alimentarias, Instituto de Física, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia;
| |
Collapse
|
15
|
Role of physical nucleation theory in understanding conformational conversion between pathogenic and nonpathogenic aggregates of low-complexity amyloid peptides. RESEARCH ON CHEMICAL INTERMEDIATES 2019. [DOI: 10.1007/s11164-019-03974-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
16
|
Arispe N, De Maio A. Memory Loss and the Onset of Alzheimer's Disease Could Be Under the Control of Extracellular Heat Shock Proteins. J Alzheimers Dis 2019; 63:927-934. [PMID: 29689729 DOI: 10.3233/jad-180161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Alzheimer's disease (AD) is a major contemporary and escalating malady in which amyloid-β (Aβ) peptides are the most likely causative agent. Aβ peptides spontaneously tend to aggregate in extracellular fluids following a progression from a monomeric state, through intermediate forms, ending in amyloid fibers and plaques. It is generally accepted now that the neurotoxic agents leading to cellular death, memory loss, and other AD characteristics are the Aβ intermediate aggregated states. However, Aβ peptides are continuously produced, released into the extracellular space, and rapidly cleared from healthy brains. Coincidentally, members of the heat shock proteins (hsp) family are present in the extracellular medium of healthy cells and body fluids, opening the possibility that hsps and Aβ could meet and interact in the extracellular milieu of the brain. In this perspective and reflection article, we place our investigation showing that the presence of Hsp70s mitigate the formation of low molecular weight Aβ peptide oligomers resulting in a reduction of cellular toxicity, in context of the current understanding of the disease. We propose that it may be an inverse relationship between the presence of Hsp70, the stage of Aβ oligomers, neurotoxicity, and the incidence of AD, particularly since the expression and circulating levels of hsp decrease with aging. Combining these observations, we propose that changes in the dynamics of Hsp70s and Aβ concentrations in the circulating brain fluids during aging defines the control of the formation of Aβ toxic aggregates, thus determining the conditions for neuron degeneration and the incidence of AD.
Collapse
Affiliation(s)
- Nelson Arispe
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Antonio De Maio
- Department of Surgery and Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| |
Collapse
|
17
|
Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
Collapse
Affiliation(s)
- Melanie P. Muller
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chang Sun
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Muyun Lihan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shashank Pant
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anda Trifan
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology
- Department of Biochemistry
- Center for Biophysics and Quantitative Biology
- College of Medicine
- University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
18
|
Belfiore M, Cariati I, Matteucci A, Gaddini L, Macchia G, Fioravanti R, Frank C, Tancredi V, D'Arcangelo G, Diociaiuti M. Calcitonin native prefibrillar oligomers but not monomers induce membrane damage that triggers NMDA-mediated Ca 2+-influx, LTP impairment and neurotoxicity. Sci Rep 2019; 9:5144. [PMID: 30914688 PMCID: PMC6435710 DOI: 10.1038/s41598-019-41462-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/08/2019] [Indexed: 01/20/2023] Open
Abstract
Amyloid protein misfolding results in a self-assembling aggregation process, characterized by the formation of typical aggregates. The attention is focused on pre-fibrillar oligomers (PFOs), formed in the early stages and supposed to be neurotoxic. PFOs structure may change due to their instability and different experimental protocols. Consequently, it is difficult to ascertain which aggregation species are actually neurotoxic. We used salmon Calcitonin (sCT) as an amyloid model whose slow aggregation rate allowed to prepare stable samples without photochemical cross-linking. Intracellular Ca2+ rise plays a fundamental role in amyloid protein-induced neurodegerations. Two paradigms have been explored: (i) the "membrane permeabilization" due to the formation of amyloid pores or other types of membrane damage; (ii) "receptor-mediated" modulation of Ca2+ channels. In the present paper, we tested the effects of native sCT PFOs- with respect to Monomer-enriched solutions in neurons characterized by an increasing degree of differentiation, in terms of -Ca2+-influx, cellular viability, -Long-Term Potentiation impairment, Post-Synaptic Densities and synaptophysin expression. Results indicated that PFOs-, but not Monomer-enriched solutions, induced abnormal -Ca2+-influx, which could only in part be ascribed to NMDAR activation. Thus, we propose an innovative neurotoxicity mechanism for amyloid proteins where "membrane permeabilization" and "receptor-mediated" paradigms coexist.
Collapse
Affiliation(s)
- Marcello Belfiore
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Ida Cariati
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Andrea Matteucci
- National Center for Drug Research and Evalutation, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Gaddini
- National Center for Drug Research and Evalutation, Istituto Superiore di Sanità, Rome, Italy
| | | | - Raoul Fioravanti
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy.,Chemistry Department, University "Sapienza", Rome, Italy
| | - Claudio Frank
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Virginia Tancredi
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Marco Diociaiuti
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy.
| |
Collapse
|
19
|
Structure of amyloid β 25-35 in lipid environment and cholesterol-dependent membrane pore formation. Sci Rep 2019; 9:2689. [PMID: 30804528 PMCID: PMC6389947 DOI: 10.1038/s41598-019-38749-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/08/2019] [Indexed: 01/14/2023] Open
Abstract
The amyloid β (Aβ) peptide and its shorter variants, including a highly cytotoxic Aβ25–35 peptide, exert their neurotoxic effect during Alzheimer’s disease by various mechanisms, including cellular membrane permeabilization. The intrinsic polymorphism of Aβ has prevented the identification of the molecular basis of Aβ pore formation by direct structural methods, and computational studies have led to highly divergent pore models. Here, we have employed a set of biophysical techniques to directly monitor Ca2+-transporting Aβ25–35 pores in lipid membranes, to quantitatively characterize pore formation, and to identify the key structural features of the pore. Moreover, the effect of membrane cholesterol on pore formation and the structure of Aβ25–35 has been elucidated. The data suggest that the membrane-embedded peptide forms 6- or 8-stranded β-barrel like structures. The 8-stranded barrels may conduct Ca2+ ions through an inner cavity, whereas the tightly packed 6-stranded barrels need to assemble into supramolecular structures to form a central pore. Cholesterol affects Aβ25–35 pore formation by a dual mechanism, i.e., by direct interaction with the peptide and by affecting membrane structure. Collectively, our data illuminate the molecular basis of Aβ membrane pore formation, which should advance both basic and clinical research on Alzheimer’s disease and membrane-associated pathologies in general.
Collapse
|
20
|
Concentration-dependent effects of mercury and lead on Aβ42: possible implications for Alzheimer's disease. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:173-187. [PMID: 30603762 DOI: 10.1007/s00249-018-1344-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/24/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023]
Abstract
Mercury (Hg) and lead (Pb) are known to be toxic non-radioactive elements, with well-described neurotoxicology. Much evidence supports the implication of metals as potential risk cofactors in Alzheimer's disease (AD). Although the action mechanism of the two metals remains unclear, Hg and Pb toxicity in AD could depend on their ability to favour misfolding and aggregation of amyloid beta proteins (Aβs) that seem to have toxic properties, particularly in their aggregated state. In our study, we evaluated the effect of Hg and Pb both on the Aβ42 ion channel incorporated in a planar lipid membrane made up of phosphatidylcholine containing 30% cholesterol and on the secondary structure of Aβ42 in an aqueous environment. The effects of Hg and Pb on the Aβ42 peptide were observed for its channel incorporated into a membrane as well as for the peptide in solution. A decreasing Aβ42 channel frequency and the formation of large and amorphous aggregates in solution that are prone to precipitate were both dependent on metal concentration. These experimental data suggest that Hg and Pb interact directly with Aβs, strengthening the hypothesis that the two metals may be a risk factor in AD.
Collapse
|
21
|
Sahoo BR, Genjo T, Bekier M, Cox SJ, Stoddard AK, Ivanova M, Yasuhara K, Fierke CA, Wang Y, Ramamoorthy A. Alzheimer's amyloid-beta intermediates generated using polymer-nanodiscs. Chem Commun (Camb) 2018; 54:12883-12886. [PMID: 30379172 PMCID: PMC6247814 DOI: 10.1039/c8cc07921h] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polymethacrylate-copolymer (PMA) encased lipid-nanodiscs (∼10 nm) and macro-nanodiscs (>15 nm) are used to study Aβ1-40 aggregation. We demonstrate that PMA-nanodiscs form a ternary association with Aβ and regulate its aggregation kinetics by trapping intermediates. Results demonstrating the reduced neurotoxicity of nanodisc-bound Aβ oligomers are also reported.
Collapse
Affiliation(s)
- Bikash R. Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Takuya Genjo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Michael Bekier
- Department of Neurology, Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Sarah J. Cox
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Andrea K. Stoddard
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Magdalena Ivanova
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Kazuma Yasuhara
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 6300192, Japan
| | - Carol A. Fierke
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
- Texas A&M University, College Station, TX 77843, USA
| | - Yanzhuang Wang
- Department of Neurology, Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| |
Collapse
|
22
|
Rivera I, Capone R, Cauvi DM, Arispe N, De Maio A. Modulation of Alzheimer's amyloid β peptide oligomerization and toxicity by extracellular Hsp70. Cell Stress Chaperones 2018; 23:269-279. [PMID: 28956268 PMCID: PMC5823807 DOI: 10.1007/s12192-017-0839-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder leading to dementia caused by advanced neuronal dysfunction and death. The most significant symptoms of AD are observed at late stages of the disease when interventions are most likely too late to ameliorate the condition. Currently, the predominant theory for AD is the "amyloid hypothesis," which states that abnormally increased levels of amyloid β (Aβ) peptides result in the production of a variety of aggregates that are neurotoxic. The specific mechanisms for Aβ peptide-induced cytotoxicity have not yet been completely elucidated. However, since the majority of Aβ is released into the extracellular milieu, it is reasonable to assume that toxicity begins outside the cells and makes its way inside where it disrupts the basic cellular process resulting in cell death. There is increasing evidence that hsp, particularly Hsp70, are exported into the extracellular milieu by an active export mechanism independent of cell death. Therefore, both Aβ peptides and Hsp70 may coexist in a common environment during pathological conditions. We observed that Hsp70 affected the Aβ assembling process in vitro preventing oligomer formation. Moreover, the presence of Hsp70 reduced the Aβ peptide-induced toxicity of cultured neurons (N2A cells). These results suggest a potential mechanism for the reduction of the detrimental effects of Aβ peptides in AD.
Collapse
Affiliation(s)
- Isabel Rivera
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA
- Initiative for Maximizing Student Development (IMSD) Program, University of California San Diego, La Jolla, CA, USA
| | - Ricardo Capone
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA
| | - David M Cauvi
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA
| | - Nelson Arispe
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
| | - Antonio De Maio
- Division of Trauma, Critical Care, Burns and Acute Care Surgery, Department of Surgery and Department of Neurosciences, School of Medicine, University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, 92093-0739, CA, USA.
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
Ho JJ, Ghosh A, Zhang TO, Zanni MT. Heterogeneous Amyloid β-Sheet Polymorphs Identified on Hydrogen Bond Promoting Surfaces Using 2D SFG Spectroscopy. J Phys Chem A 2018; 122:1270-1282. [DOI: 10.1021/acs.jpca.7b11934] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jia-Jung Ho
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Ayanjeet Ghosh
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tianqi O. Zhang
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
25
|
Kandel N, Zheng T, Huo Q, Tatulian SA. Membrane Binding and Pore Formation by a Cytotoxic Fragment of Amyloid β Peptide. J Phys Chem B 2017; 121:10293-10305. [PMID: 29039658 DOI: 10.1021/acs.jpcb.7b07002] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloid β (Aβ) peptide contributes to Alzheimer's disease by a yet unidentified mechanism. In the brain tissue, Aβ occurs in various forms, including an undecapeptide Aβ25-35, which exerts a neurotoxic effect through the mitochondrial dysfunction and/or Ca2+-permeable pore formation in cell membranes. This work was aimed at the biophysical characterization of membrane binding and pore formation by Aβ25-35. Interaction of Aβ25-35 with anionic and zwitterionic membranes was analyzed by microelectrophoresis. In pore formation experiments, Aβ25-35 was incubated in aqueous buffer to form oligomers and added to Quin-2-loaded vesicles. Gradual increase in Quin-2 fluorescence was interpreted in terms of membrane pore formation by the peptide, Ca2+ influx, and binding to intravesicular Quin-2. The kinetics and magnitude of this process were used to evaluate the rate constant of pore formation, peptide-peptide association constants, and the oligomeric state of the pores. Decrease in membrane anionic charge and high ionic strength conditions significantly suppressed membrane binding and pore formation, indicating the importance of electrostatic interactions in these events. Circular dichroism spectroscopy showed that Aβ25-35 forms the most efficient pores in β-sheet conformation. The data are consistent with an oligo-oligomeric pore model composed of up to eight peptide units, each containing 6-8 monomers.
Collapse
Affiliation(s)
| | | | | | - Suren A Tatulian
- Department of Physics, University of Central Florida , Physical Sciences Bldg., Room 456, 4111 Libra Drive, Orlando, Florida 32816, United States
| |
Collapse
|
26
|
Voelker MJ, Barz B, Urbanc B. Fully Atomistic Aβ40 and Aβ42 Oligomers in Water: Observation of Porelike Conformations. J Chem Theory Comput 2017; 13:4567-4583. [DOI: 10.1021/acs.jctc.7b00495] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Matthew J. Voelker
- Department
of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Bogdan Barz
- Institute
of Complex Systems, Structural Biochemistry ICS-6: Structural Biochemistry, Forschungzentrum Jülich GmbH, Jülich 52425, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Brigita Urbanc
- Department
of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
- Faculty
of Mathematics and Physics, University of Ljubljana, Ljubljana 1000, Slovenia
| |
Collapse
|
27
|
Abstract
Aggregation of the amyloid-β (Aβ) peptide is strongly correlated with Alzheimer's disease (AD). Recent research has improved our understanding of the kinetics of amyloid fibril assembly and revealed new details regarding different stages in plaque formation. Presently, interest is turning toward studying this process in a holistic context, focusing on cellular components which interact with the Aβ peptide at various junctures during aggregation, from monomer to cross-β amyloid fibrils. However, even in isolation, a multitude of factors including protein purity, pH, salt content, and agitation affect Aβ fibril formation and deposition, often producing complicated and conflicting results. The failure of numerous inhibitors in clinical trials for AD suggests that a detailed examination of the complex interactions that occur during plaque formation, including binding of carbohydrates, lipids, nucleic acids, and metal ions, is important for understanding the diversity of manifestations of the disease. Unraveling how a variety of key macromolecular modulators interact with the Aβ peptide and change its aggregation properties may provide opportunities for developing therapies. Since no protein acts in isolation, the interplay of these diverse molecules may differentiate disease onset, progression, and severity, and thus are worth careful consideration.
Collapse
Affiliation(s)
- Katie L Stewart
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
28
|
Aβ42 assembles into specific β-barrel pore-forming oligomers in membrane-mimicking environments. Proc Natl Acad Sci U S A 2016; 113:10866-71. [PMID: 27621459 DOI: 10.1073/pnas.1605104113] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The formation of amyloid-β peptide (Aβ) oligomers at the cellular membrane is considered to be a crucial process underlying neurotoxicity in Alzheimer's disease (AD). Therefore, it is critical to characterize the oligomers that form within a membrane environment. To contribute to this characterization, we have applied strategies widely used to examine the structure of membrane proteins to study the two major Aβ variants, Aβ40 and Aβ42. Accordingly, various types of detergent micelles were extensively screened to identify one that preserved the properties of Aβ in lipid environments-namely the formation of oligomers that function as pores. Remarkably, under the optimized detergent micelle conditions, Aβ40 and Aβ42 showed different behavior. Aβ40 aggregated into amyloid fibrils, whereas Aβ42 assembled into oligomers that inserted into lipid bilayers as well-defined pores and adopted a specific structure with characteristics of a β-barrel arrangement that we named β-barrel pore-forming Aβ42 oligomers (βPFOsAβ42). Because Aβ42, relative to Aβ40, has a more prominent role in AD, the higher propensity of Aβ42 to form βPFOs constitutes an indication of their relevance in AD. Moreover, because βPFOsAβ42 adopt a specific structure, this property offers an unprecedented opportunity for testing a hypothesis regarding the involvement of βPFOs and, more generally, membrane-associated Aβ oligomers in AD.
Collapse
|
29
|
Common molecular mechanism of amyloid pore formation by Alzheimer's β-amyloid peptide and α-synuclein. Sci Rep 2016; 6:28781. [PMID: 27352802 PMCID: PMC4926208 DOI: 10.1038/srep28781] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/08/2016] [Indexed: 12/16/2022] Open
Abstract
Calcium-permeable pores formed by small oligomers of amyloid proteins are the primary pathologic species in Alzheimer’s and Parkinson’s diseases. However, the molecular mechanisms underlying the assembly of these toxic oligomers in the plasma membrane of brain cells remain unclear. Here we have analyzed and compared the pore-forming capability of a large panel of amyloid proteins including wild-type, variant and truncated forms, as well as synthetic peptides derived from specific domains of Aβ1-42 and α-synuclein. We show that amyloid pore formation involves two membrane lipids, ganglioside and cholesterol, that physically interact with amyloid proteins through specific structural motifs. Mutation or deletion of these motifs abolished pore formation. Moreover, α-synuclein (Parkinson) and Aβ peptide (Alzheimer) did no longer form Ca2+-permeable pores in presence of drugs that target either cholesterol or ganglioside or both membrane lipids. These results indicate that gangliosides and cholesterol cooperate to favor the formation of amyloid pores through a common molecular mechanism that can be jammed at two different steps, suggesting the possibility of a universal therapeutic approach for neurodegenerative diseases. Finally we present the first successful evaluation of such a new therapeutic approach (coined “membrane therapy”) targeting amyloid pores formed by Aβ1-42 and α-synuclein.
Collapse
|
30
|
Zulpo M, Kotulska M. Comparative modeling of hypothetical amyloid pores based on cylindrin. J Mol Model 2015; 21:151. [PMID: 25994458 DOI: 10.1007/s00894-015-2691-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/27/2015] [Indexed: 12/14/2022]
Abstract
Cylindrin is a six-stranded antiparallel beta barrel obtained from amyloidogenic strands of crystallin. It induces cell toxicity through an unknown mechanism. In this work, the potential use of the structure of cylindrin as a template for modeling amyloid pores-hypothetical transmembrane structures which appear during amyloid diseases-was studied. Using comparative modeling (performed by Modeller), we tested the stability of cylindrin-based pores made from several amyloid-forming and non-amyloid-forming strands deriving from mutated cylindrin and the prion sup35. We showed that cylindrin could be used as a template for modeling pores made from strands of amyloid proteins, but that the cylindrin structure does not result from the amyloidogenicity of these fragments, as fibril non-formers from the prion were also able to form a similar structure. Finally, we tested whether the cellular toxicity of cylindrin and related structures could be due to its incorporation into the cell membrane, leading to the creation of conducting ionic channels. The results of modeling indicate that cylindrin and tandem-repeat cylindrin, mutants of them, and cylindrin-like amyloid pores from prion sequences can only localize on the periphery of the membrane, and are not able to conduct any ions into the cell. These findings explain experimental results obtained for large unilamellar vesicles incubated with cylindrin, where conductance was not observed.
Collapse
Affiliation(s)
- Magdalena Zulpo
- Department of Biomedical Engineering, Wroclaw University of Technology, ul. Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | | |
Collapse
|
31
|
Alred EJ, Phillips M, Berhanu WM, Hansmann UHE. On the lack of polymorphism in Aβ-peptide aggregates derived from patient brains. Protein Sci 2015; 24:923-35. [PMID: 25739352 DOI: 10.1002/pro.2668] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/11/2015] [Accepted: 02/15/2015] [Indexed: 11/09/2022]
Abstract
The amyloid beta (Aβ) oligomers and fibrils that are found in neural tissues of patients suffering from Alzheimer's disease may either cause or contribute to the pathology of the disease. In vitro, these Aβ-aggregates are characterized by structural polymorphism. However, recent solid state NMR data of fibrils acquired post mortem from the brains of two Alzheimer's patients indicate presence of only a single, patient-specific structure. Using enhanced molecular dynamic simulations we investigate the factors that modulate the stability of Aβ-fibrils. We find characteristic differences in molecular flexibility, dynamics of interactions, and structural behavior between the brain-derived Aβ-fibril structure and in vitro models. These differences may help to explain the lack of polymorphism in fibrils collected from patient brains, and have to be taken into account when designing aggregation inhibitors and imaging agents for Alzheimer's disease.
Collapse
Affiliation(s)
- Erik J Alred
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019
| | - Malachi Phillips
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019
| | - Workalemahu M Berhanu
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019
| | - Ulrich H E Hansmann
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019
| |
Collapse
|
32
|
Lipids in Amyloid-β Processing, Aggregation, and Toxicity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:67-94. [PMID: 26149926 DOI: 10.1007/978-3-319-17344-3_3] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aggregation of amyloid-beta (Aβ) peptide is the major event underlying neuronal damage in Alzheimer's disease (AD). Specific lipids and their homeostasis play important roles in this and other neurodegenerative disorders. The complex interplay between the lipids and the generation, clearance or deposition of Aβ has been intensively investigated and is reviewed in this chapter. Membrane lipids can have an important influence on the biogenesis of Aβ from its precursor protein. In particular, increased cholesterol in the plasma membrane augments Aβ generation and shows a strong positive correlation with AD progression. Furthermore, apolipoprotein E, which transports cholesterol in the cerebrospinal fluid and is known to interact with Aβ or compete with it for the lipoprotein receptor binding, significantly influences Aβ clearance in an isoform-specific manner and is the major genetic risk factor for AD. Aβ is an amphiphilic peptide that interacts with various lipids, proteins and their assemblies, which can lead to variation in Aβ aggregation in vitro and in vivo. Upon interaction with the lipid raft components, such as cholesterol, gangliosides and phospholipids, Aβ can aggregate on the cell membrane and thereby disrupt it, perhaps by forming channel-like pores. This leads to perturbed cellular calcium homeostasis, suggesting that Aβ-lipid interactions at the cell membrane probably trigger the neurotoxic cascade in AD. Here, we overview the roles of specific lipids, lipid assemblies and apolipoprotein E in Aβ processing, clearance and aggregation, and discuss the contribution of these factors to the neurotoxicity in AD.
Collapse
|
33
|
Di Scala C, Chahinian H, Yahi N, Garmy N, Fantini J. Interaction of Alzheimer's β-amyloid peptides with cholesterol: mechanistic insights into amyloid pore formation. Biochemistry 2014; 53:4489-502. [PMID: 25000142 DOI: 10.1021/bi500373k] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Brain cholesterol plays a critical role in Alzheimer's disease and other neurodegenerative diseases. The molecular mechanisms linking cholesterol to neurotoxicity have remained elusive for a long time, but recent data have allowed the identification of functional cholesterol-binding domains in several amyloidogenic proteins involved in neurodegenerative diseases, including Alzheimer's disease. In this review, we analyze the cholesterol binding properties of β-amyloid (Aβ) peptides and the impact of these interactions on amyloid pore formation. We show that although the cholesterol-binding domains of Aβ peptides and of transmembrane precursor C99 are partially overlapping, they involve distinct amino acid residues, so that cholesterol has a greater affinity for Aβ than for C99. Synthetic 22-35 and 25-35 fragments of Aβ retained the ability of the full-length peptide 1-42 to bind cholesterol and to form zinc-sensitive, calcium-permeable amyloid pores in cultured neural cells. Studies with mutant peptides allowed the identification of key residues involved in cholesterol binding and channel formation. Cholesterol promoted the insertion of Aβ in the plasma membrane, induced α-helical structuration, and forced the peptide to adopt a tilted topology that favored the oligomerization process. Bexarotene, an amphipathic drug currently considered as a potential candidate medication for the treatment of neurodegenerative diseases, competed with cholesterol for binding to Aβ and prevented oligomeric channel formation. These studies indicate that it is possible to prevent the generation of neurotoxic oligomers by targeting the cholesterol-binding domain of Aβ peptides. This original strategy could be used for the treatment of Alzheimer's and other neurodegenerative diseases that involve cholesterol-dependent toxic oligomers.
Collapse
Affiliation(s)
- Coralie Di Scala
- EA-4674, Faculté des Sciences de Saint-Jérôme, Aix-Marseille Université , 13013 Marseille, France
| | | | | | | | | |
Collapse
|
34
|
Notarachille G, Arnesano F, Calò V, Meleleo D. Heavy metals toxicity: effect of cadmium ions on amyloid beta protein 1-42. Possible implications for Alzheimer's disease. Biometals 2014; 27:371-88. [PMID: 24557150 DOI: 10.1007/s10534-014-9719-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/12/2014] [Indexed: 02/02/2023]
Abstract
Cadmium (Cd) is an environmental contaminant, highly toxic to humans. This biologically non-essential element accumulates in the body, especially in the kidney, liver, lung and brain and can induce several toxic effects, depending on the concentration and the exposure time. Cd has been linked to Alzheimer's disease (AD) as a probable risk factor, as it shows higher concentrations in brain tissues of AD patients than in healthy people, its implication in the formation of neurofibrillary tangles and in the aggregation process of amyloid beta peptides (AβPs). AβPs seem to have toxic properties, particularly in their aggregated state; insoluble AβP forms, such as small and large aggregates, protofibrils and fibrils, appear to be implicated in the pathogenesis of AD. In our study, we have evaluated the effect of Cd, at different concentrations, both on the AβP1-42 ion channel incorporated in a planar lipid membrane made up of phosphatidylcholine containing 30 % cholesterol and on the secondary structure of AβP1-42 in aqueous environment. Cadmium is able to interact with the AβP1-42 peptide by acting on the channel incorporated into the membrane as well as on the peptide in solution, both decreasing AβP1-42 channel frequency and in solution forming large and amorphous aggregates prone to precipitate. These experimental observations suggesting a toxic role for Cd strengthen the hypothesis that Cd may interact directly with AβPs and may be a risk factor in AD.
Collapse
Affiliation(s)
- Gabriella Notarachille
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", via E. Orabona 4, 70126, Bari, Italy
| | | | | | | |
Collapse
|
35
|
Kawahara M, Mizuno D, Koyama H, Konoha K, Ohkawara S, Sadakane Y. Disruption of zinc homeostasis and the pathogenesis of senile dementia. Metallomics 2014; 6:209-19. [DOI: 10.1039/c3mt00257h] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
36
|
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.
Collapse
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:
| |
Collapse
|
37
|
ATR-FTIR: A “rejuvenated” tool to investigate amyloid proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2328-38. [DOI: 10.1016/j.bbamem.2013.04.012] [Citation(s) in RCA: 263] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/20/2013] [Accepted: 04/02/2013] [Indexed: 12/24/2022]
|
38
|
Zhao LN, Mu Y, Chew LY. Heme prevents amyloid beta peptide aggregation through hydrophobic interaction based on molecular dynamics simulation. Phys Chem Chem Phys 2013; 15:14098-106. [PMID: 23868536 DOI: 10.1039/c3cp52354c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Heme, which is abundant in hemoglobin and many other hemoproteins, is known to play an important role in electron transfer, oxygen transport, regulation of gene expression, and many other biological functions. With the belief that the aggregation of Aβ peptides forming higher order oligomers is one of the central pathological pathways in Alzheimer's disease, the formation of the Aβ-heme complex is essential as it inhibits Aβ aggregation and protects the neurons from degradation. In our studies, conventional molecular dynamics simulations were performed on the 1 Aβ + 1 heme and 2 Aβ + 4 hemes system, respectively, with the identification of several dominant binding motifs. We found that hydrophobic residues of the Aβ peptide have a high affinity to interact with heme instead of the histidine residue. We conclude that hydrophobic interaction plays a dominant role in the Aβ-heme complex formation which indirectly serves to physically prevent Aβ aggregation.
Collapse
Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical Sciences, Nanyang Technological University, Nanyang Link 21, Singapore
| | | | | |
Collapse
|
39
|
AβP1-42 incorporation and channel formation in planar lipid membranes: the role of cholesterol and its oxidation products. J Bioenerg Biomembr 2013; 45:369-81. [DOI: 10.1007/s10863-013-9513-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/12/2013] [Indexed: 02/06/2023]
|
40
|
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]
|
41
|
Gallion SL. Modeling amyloid-beta as homogeneous dodecamers and in complex with cellular prion protein. PLoS One 2012; 7:e49375. [PMID: 23145167 PMCID: PMC3493521 DOI: 10.1371/journal.pone.0049375] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/11/2012] [Indexed: 12/16/2022] Open
Abstract
Soluble amyloid beta (Aβ) peptide has been linked to the pathology of Alzheimer's disease. A variety of soluble oligomers have been observed to be toxic, ranging from dimers to protofibrils. No tertiary structure has been identified as a single biologically relevant form, though many models are comprised of highly ordered β-sheets. Evidence exists for much less ordered toxic oligomers. The mechanism of toxicity remains highly debated and probably involves multiple pathways. Interaction of Aβ oligomers with the N-terminus of the cellular form of the prion protein (PrP(c)) has recently been proposed. The intrinsically disordered nature of this protein and the highly polymorphic nature of Aβ oligomers make structural resolution of the complex exceptionally challenging. In this study, molecular dynamics simulations are performed for dodecameric assemblies of Aβ comprised of monomers having a single, short antiparallel β-hairpin at the C-terminus. The resulting models, devoid of any intermolecular hydrogen bonds, are shown to correlate well with experimental data and are found to be quite stable within the hydrophobic core, whereas the α-helical N-termini transform to a random coil state. This indicates that highly ordered assemblies are not required for stability and less ordered oligomers are a viable component in the population of soluble oligomers. In addition, a tentative model is proposed for the association of Aβ dimers with a double deletion mutant of the intrinsically disordered N-terminus of PrP(c). This may be useful as a conceptual working model for the binding of higher order oligomers and in the design of further experiments.
Collapse
|
42
|
Prangkio P, Yusko EC, Sept D, Yang J, Mayer M. Multivariate analyses of amyloid-beta oligomer populations indicate a connection between pore formation and cytotoxicity. PLoS One 2012; 7:e47261. [PMID: 23077580 PMCID: PMC3471831 DOI: 10.1371/journal.pone.0047261] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/07/2012] [Indexed: 11/18/2022] Open
Abstract
Aggregates of amyloid-beta (Aβ) peptides are thought to be involved in the development of Alzheimer's disease because they can change synaptic plasticity and induce neuronal cell death by inflammation, oxidative damage, and transmembrane pore formation. Exactly which oligomeric species underlie these cytotoxic effects remains unclear. The work presented here established well-controlled aggregation conditions of Aβ₁₋₄₀ or Aβ₁₋₄₂ peptides over a 20-day period and characterized these preparations with regard to their β-sheet content, degree of fibril formation, relative abundance of various oligomer sizes, and propensity to induce membrane pore formation and cytotoxicity. Using this multivariate data set, a systematic and inherently unbiased partial least squares (PLS) approach showed that for both peptides the abundance of oligomers in the tetramer to 13-mer range contributed positively to both pore formation and cytotoxicity, while monomers, dimers, trimers, and the largest oligomers (>210 kDa) were negatively correlated to both phenomena. Multivariate PLS analysis is ideally suited to handle complex data sets and interdependent variables such as relative oligomer concentrations, making it possible to elucidate structure function relationships in complex mixtures. This approach, therefore, introduces an enabling tool to the field of amyloid research, in which it is often difficult to interpret the activity of individual species within a complex mixture of bioactive species.
Collapse
Affiliation(s)
- Panchika Prangkio
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | | | | | | |
Collapse
|
43
|
Zhao LN, Chiu SW, Benoit J, Chew LY, Mu Y. The Effect of Curcumin on the Stability of Aβ Dimers. J Phys Chem B 2012; 116:7428-35. [DOI: 10.1021/jp3034209] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical
Sciences, Nanyang Technological University
| | - See-Wing Chiu
- Beckman Institute, University of Illinois, Urbana, Illinois
| | - Jérôme Benoit
- School of Physical and Mathematical
Sciences, Nanyang Technological University
| | - Lock Yue Chew
- School of Physical and Mathematical
Sciences, Nanyang Technological University
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore
| |
Collapse
|
44
|
Zhao LN, Long H, Mu Y, Chew LY. The toxicity of amyloid β oligomers. Int J Mol Sci 2012; 13:7303-7327. [PMID: 22837695 PMCID: PMC3397527 DOI: 10.3390/ijms13067303] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 12/13/2022] Open
Abstract
In this review, we elucidate the mechanisms of Aβ oligomer toxicity which may contribute to Alzheimer's disease (AD). In particular, we discuss on the interaction of Aβ oligomers with the membrane through the process of adsorption and insertion. Such interaction gives rises to phase transitions in the sub-structures of the Aβ peptide from α-helical to β-sheet structure. By means of a coarse-grained model, we exhibit the tendency of β-sheet structures to aggregate, thus providing further insights to the process of membrane induced aggregation. We show that the aggregated oligomer causes membrane invagination, which is a precursor to the formation of pore structures and ion channels. Other pathological progressions to AD due to Aβ oligomers are also covered, such as their interaction with the membrane receptors, and their direct versus indirect effects on oxidative stress and intraneuronal accumulation. We further illustrate that the molecule curcumin is a potential Aβ toxicity inhibitor as a β-sheet breaker by having a high propensity to interact with certain Aβ residues without binding to them. The comprehensive understanding gained from these current researches on the various toxicity mechanisms show promises in the provision of better therapeutics and treatment strategies in the near future.
Collapse
Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
| | - HonWai Long
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
- High Performance Computing Centre, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Lock Yue Chew
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
| |
Collapse
|
45
|
Capone R, Jang H, Kotler SA, Connelly L, Teran Arce F, Ramachandran S, Kagan BL, Nussinov R, Lal R. All-d-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers. J Chem Theory Comput 2012; 8:1143-1152. [PMID: 22423218 PMCID: PMC3302213 DOI: 10.1021/ct200885r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Indexed: 12/11/2022]
Abstract
Alzheimer's disease (AD) is the most common type of senile dementia in aging populations. Amyloid β (Aβ)-mediated dysregulation of ionic homeostasis is the prevailing underlying mechanism leading to synaptic degeneration and neuronal death. Aβ-dependent ionic dysregulation most likely occurs either directly via unregulated ionic transport through the membrane or indirectly via Aβ binding to cell membrane receptors and subsequent opening of existing ion channels or transporters. Receptor binding is expected to involve a high degree of stereospecificity. Here, we investigated whether an Aβ peptide enantiomer, whose entire sequence consists of d-amino acids, can form ion-conducting channels; these channels can directly mediate Aβ effects even in the absence of receptor-peptide interactions. Using complementary approaches of planar lipid bilayer (PLB) electrophysiological recordings and molecular dynamics (MD) simulations, we show that the d-Aβ isomer exhibits ion conductance behavior in the bilayer indistinguishable from that described earlier for the l-Aβ isomer. The d isomer forms channel-like pores with heterogeneous ionic conductance similar to the l-Aβ isomer channels, and the d-isomer channel conductance is blocked by Zn(2+), a known blocker of l-Aβ isomer channels. MD simulations further verify formation of β-barrel-like Aβ channels with d- and l-isomers, illustrating that both d- and l-Aβ barrels can conduct cations. The calculated values of the single-channel conductance are approximately in the range of the experimental values. These findings are in agreement with amyloids forming Ca(2+) leaking, unregulated channels in AD, and suggest that Aβ toxicity is mediated through a receptor-independent, nonstereoselective mechanism.
Collapse
Affiliation(s)
- Ricardo Capone
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Incorporated,
NCI-Frederick, Frederick, Maryland 21702, United States
| | - Samuel A. Kotler
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Laura Connelly
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Fernando Teran Arce
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| | - Srinivasan Ramachandran
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, 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—Los Angeles, Los Angeles, California 90024, United States
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Incorporated,
NCI-Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular
Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Departments of Bioengineering
and Mechanical and Aerospace Engineering and Material Science Program, University of California—San Diego, La Jolla,
California 92093, United States
| |
Collapse
|
46
|
Laganowsky A, Liu C, Sawaya MR, Whitelegge JP, Park J, Zhao M, Pensalfini A, Soriaga A, Landau M, Teng PK, Cascio D, Glabe C, Eisenberg D. Atomic view of a toxic amyloid small oligomer. Science 2012; 335:1228-31. [PMID: 22403391 PMCID: PMC3959867 DOI: 10.1126/science.1213151] [Citation(s) in RCA: 467] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid diseases, including Alzheimer's, Parkinson's, and the prion conditions, are each associated with a particular protein in fibrillar form. These amyloid fibrils were long suspected to be the disease agents, but evidence suggests that smaller, often transient and polymorphic oligomers are the toxic entities. Here, we identify a segment of the amyloid-forming protein αB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: β-sheet-rich structure, cytotoxicity, and recognition by an oligomer-specific antibody. The x-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six antiparallel protein strands, that we term a cylindrin. The cylindrin structure is compatible with a sequence segment from the β-amyloid protein of Alzheimer's disease. Cylindrins offer models for the hitherto elusive structures of amyloid oligomers.
Collapse
Affiliation(s)
- Arthur Laganowsky
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Cong Liu
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Julian P. Whitelegge
- The NPI-Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, USA
| | - Jiyong Park
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Minglei Zhao
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Anna Pensalfini
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - Angela Soriaga
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Meytal Landau
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Poh K. Teng
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Duilio Cascio
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| | - Charles Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
| | - David Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE, Institute for Genomics and Proteomics, Departments of Biological Chemistry and Chemistry & Biochemistry, Los Angeles, California, USA
| |
Collapse
|
47
|
Connelly L, Arce FT, Jang H, Capone R, Kotler SA, Ramachandran S, Kagan BL, Nussinov R, Lal R. Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's β-amyloid peptide: relevance to the ion channel mechanism of AD pathology. J Phys Chem B 2012; 116:1728-35. [PMID: 22217000 PMCID: PMC4342054 DOI: 10.1021/jp2108126] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is a protein misfolding disease characterized by a buildup of β-amyloid (Aβ) peptide as senile plaques, uncontrolled neurodegeneration, and memory loss. AD pathology is linked to the destabilization of cellular ionic homeostasis and involves Aβ peptide-plasma membrane interactions. In principle, there are two possible ways through which disturbance of the ionic homeostasis can take place: directly, where the Aβ peptide either inserts into the membrane and creates ion-conductive pores or destabilizes the membrane organization, or, indirectly, where the Aβ peptide interacts with existing cell membrane receptors. To distinguish between these two possible types of Aβ-membrane interactions, we took advantage of the biochemical tenet that ligand-receptor interactions are stereospecific; L-amino acid peptides, but not their D-counterparts, bind to cell membrane receptors. However, with respect to the ion channel-mediated mechanism, like L-amino acids, D-amino acid peptides will also form ion channel-like structures. Using atomic force microscopy (AFM), we imaged the structures of both D- and L-enantiomers of the full length Aβ(1-42) when reconstituted in lipid bilayers. AFM imaging shows that both L- and D-Aβ isomers form similar channel-like structures. Molecular dynamics (MD) simulations support the AFM imaged 3D structures. Previously, we have shown that D-Aβ(1-42) channels conduct ions similarly to their L- counterparts. Taken together, our results support the direct mechanism of Aβ ion channel-mediated destabilization of ionic homeostasis rather than the indirect mechanism through Aβ interaction with membrane receptors.
Collapse
Affiliation(s)
- Laura Connelly
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Materials Science Program, University of California, San Diego, La Jolla, CA 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, CA 92093, USA
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Ricardo Capone
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Materials Science Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel A. Kotler
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Materials Science Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Srinivasan Ramachandran
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and 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 Human Behavior, University of California, Los Angeles, CA 90024, USA
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - Ratnesh Lal
- Departments of Bioengineering and of Mechanical and Aerospace Engineering and Materials Science Program, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
48
|
Oliveira LT, Matos PA, Provance DW, de Mello FG, Andrade LR, Sorenson MM, Salerno VP. β-amyloid peptide is internalized into chick retinal neurons and alters the distribution of myosin Vb. Cytoskeleton (Hoboken) 2012; 69:166-78. [DOI: 10.1002/cm.21007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 12/22/2011] [Accepted: 01/03/2012] [Indexed: 11/07/2022]
|
49
|
Capone R, Jang H, Kotler S, Kagan BL, Nussinov R, Lal R. Probing structural features of Alzheimer's amyloid-β pores in bilayers using site-specific amino acid substitutions. Biochemistry 2012; 51:776-85. [PMID: 22242635 PMCID: PMC3265145 DOI: 10.1021/bi2017427] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/29/2011] [Indexed: 11/28/2022]
Abstract
A current hypothesis for the pathology of Alzheimer's disease (AD) proposes that amyloid-β (Aβ) peptides induce uncontrolled, neurotoxic ion flux across cellular membranes. The mechanism of ion flux is not fully understood because no experiment-based Aβ channel structures at atomic resolution are currently available (only a few polymorphic states have been predicted by computational models). Structural models and experimental evidence lend support to the view that the Aβ channel is an assembly of loosely associated mobile β-sheet subunits. Here, using planar lipid bilayers and molecular dynamics (MD) simulations, we show that amino acid substitutions can be used to infer which residues are essential for channel structure. We created two Aβ(1-42) peptides with point mutations: F19P and F20C. The substitution of Phe19 with Pro inhibited channel conductance. MD simulation suggests a collapsed pore of F19P channels at the lower bilayer leaflet. The kinks at the Pro residues in the pore-lining β-strands induce blockage of the solvated pore by the N-termini of the chains. The cysteine mutant is capable of forming channels, and the conductance behavior of F20C channels is similar to that of the wild type. Overall, the mutational analysis of the channel activity performed in this work tests the proposition that the channels consist of a β-sheet rich organization, with the charged/polar central strand containing the mutation sites lining the pore, and the C-terminal strands facing the hydrophobic lipid tails. A detailed understanding of channel formation and its structure should aid studies of drug design aiming to control unregulated Aβ-dependent ion fluxes.
Collapse
Affiliation(s)
- Ricardo Capone
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
| | - Hyunbum Jang
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland 21702, United States
| | - Samuel
A. Kotler
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, 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, Los
Angeles, California 90024, United States
| | - Ruth Nussinov
- Center for Cancer Research Nanobiology
Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland 21702, United States
- Department of Human Molecular
Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ratnesh Lal
- Department of Bioengineering,
Department of Mechanical and Aerospace Engineering, and Material Science
Program, University of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
50
|
Kagan BL. Membrane pores in the pathogenesis of neurodegenerative disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 107:295-325. [PMID: 22482454 DOI: 10.1016/b978-0-12-385883-2.00001-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The neurodegenerative diseases described in this volume, as well as many nonneurodegenerative diseases, are characterized by deposits known as amyloid. Amyloid has long been associated with these various diseases as a pathological marker and has been implicated directly in the molecular pathogenesis of disease. However, increasing evidence suggests that these proteinaceous Congo red staining deposits may not be toxic or destructive of tissue. Recent studies strongly implicate smaller aggregates of amyloid proteins as the toxic species underlying these neurodegenerative diseases. Despite the outward obvious differences among these clinical syndromes, there are some striking similarities in their molecular pathologies. These include dysregulation of intracellular calcium levels, impairment of mitochondrial function, and the ability of virtually all amyloid peptides to form ion-permeable pores in lipid membranes. Pore formation is enhanced by environmental factors that promote protein aggregation and is inhibited by agents, such as Congo red, which prevent aggregation. Remarkably, the pores formed by a variety of amyloid peptides from neurodegenerative and other diseases share a common set of physiologic properties. These include irreversible insertion of the pores in lipid membranes, formation of heterodisperse pore sizes, inhibition by Congo red of pore formation, blockade of pores by zinc, and a relative lack of ion selectivity and voltage dependence. Although there exists some information about the physical structure of these pores, molecular modeling suggests that 4-6-mer amyloid subunits may assemble into 24-mer pore-forming aggregates. The molecular structure of these pores may resemble the β-barrel structure of the toxics pore formed by bacterial toxins, such as staphylococcal α-hemolysin, anthrax toxin, and Clostridium perfringolysin.
Collapse
Affiliation(s)
- Bruce L Kagan
- Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Semel Institute for Neuroscience and Human Behavior, Los Angeles, California, USA
| |
Collapse
|