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Tang Y, Zhang D, Robinson S, Zheng J. Inhibition of Pancreatic Cancer Cells by Different Amyloid Proteins Reveals an Inverse Relationship between Neurodegenerative Diseases and Cancer. Adv Biol (Weinh) 2023; 7:e2300070. [PMID: 37080947 DOI: 10.1002/adbi.202300070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/22/2023] [Indexed: 04/22/2023]
Abstract
Neurodegenerative diseases and cancers are considered to be two families of diseases caused by completely opposite cell-death mechanisms: the former caused by premature cell death, with the latter due to the increased resistance to cell death. Growing epidemiologic evidence appear to suggest an inverse correlation between neurodegenerative diseases and cancers. However, pathological links, particularly from a protein-cell interaction perspective, between these two families of diseases remains to be proven. Here, a fundamental study investigates the effects of three amyloid proteins of Aβ (associated with AD), hIAPP (associated with T2D), and hCT (associated with MTC) on pancreatic cancer (PANC-1) cells. Collective results demonstrate a general inhibitory activity of all of three amyloid proteins on cancer cell proliferation, but inhibition efficiencies are strongly dependent on amyloid sequence (Aβ, hIAPP, hCT), concentration (IC25, IC50, IC75), and aggregation states (monomers, oligomers). Amyloid proteins exhibit two pathways against cancer cells: amyloid monomer-induced ROS production to inhibit cell growth and amyloid oligomer-induced membrane disruption to kill cells. Collectively, the results demonstrate a general inhibition function of amyloid proteins to induce cancer cell death by preventing cell proliferation, suppressing cell migration, promoting reactive oxygen species production, and disrupting cell membranes.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Sarah Robinson
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
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2
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Tiwari A, Pradhan S, Sannigrahi A, Mahakud AK, Jha S, Chattopadhyay K, Biswas M, Saleem M. “Interplay of lipid-head group and packing defects in driving Amyloid-beta mediated myelin-like model membrane deformation”. J Biol Chem 2023; 299:104653. [PMID: 36990217 PMCID: PMC10148160 DOI: 10.1016/j.jbc.2023.104653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Accumulating evidence suggests that amyloid plaque associated myelin lipid loss as a result of elevated amyloid burden might also contribute to Alzheimer's disease. The amyloid fibrils though closely associated with lipids under physiological conditions, however, the progression of membrane remodeling events leading to lipid-fibril assembly remains unknown. Here we first reconstitute the interaction of Aβ-40 with myelin-like model membrane and show that the binding of Aβ-40 induces extensive tubulation. To look into the mechanism of membrane tubulation we chose a set of membrane conditions varying in lipid packing density and net charge that allows us to dissect the contribution of lipid specificity of Aβ-40 binding, aggregation kinetics, and subsequent changes in membrane parameters such as fluidity, diffusion, and compressibility modulus. We show that the binding of Aβ-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin-like model membrane during the early phase of amyloid aggregation. Furthermore, elongation of Aβ-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the model membrane followed by extensive lipid membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of Aβ-40 - myelin-like model membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril-mediated load generation results in the consequent association of lipids with growing amyloid fibrils.
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3
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Wang K, Na L, Duan M. The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β. Curr Top Med Chem 2021; 21:151-167. [PMID: 32938351 DOI: 10.2174/1568026620666200916123000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/02/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022]
Abstract
Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.
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Affiliation(s)
- Ke Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liu Na
- School of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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4
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Natesh SR, Hummels AR, Sachleben JR, Sosnick TR, Freed KF, Douglas JF, Meredith SC, Haddadian EJ. Molecular dynamics study of water channels in natural and synthetic amyloid-β fibrils. J Chem Phys 2021; 154:235102. [PMID: 34241272 PMCID: PMC8214467 DOI: 10.1063/5.0049250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 11/14/2022] Open
Abstract
We compared all-atom explicit solvent molecular dynamics simulations of three types of Aβ(1-40) fibrils: brain-seeded fibrils (2M4J, with a threefold axial symmetry) and the other two, all-synthetic fibril polymorphs (2LMN and 2LMP, made under different fibrillization conditions). Fibril models were constructed using either a finite or an infinite number of layers made using periodic images. These studies yielded four conclusions. First, finite fibrils tend to unravel in a manner reminiscent of fibril dissolution, while infinite fibrils were more stable during simulations. Second, salt bridges in these fibrils remained stable in those fibrils that contained them initially, and those without salt bridges did not develop them over the time course of the simulations. Third, all fibrils tended to develop a "stagger" or register shift of β-strands along the fibril axis. Fourth and most importantly, the brain-seeded, 2M4J, infinite fibrils allowed bidirectional transport of water in and out of the central longitudinal core of the fibril by rapidly developing gaps at the fibril vertices. 2LMP fibrils also showed this behavior, although to a lesser extent. The diffusion of water molecules in the fibril core region involved two dynamical states: a localized state and directed diffusion in the presence of obstacles. These observations provided support for the hypothesis that Aβ fibrils could act as nanotubes. At least some Aβ oligomers resembled fibrils structurally in having parallel, in-register β-sheets and a sheet-turn-sheet motif. Thus, our findings could have implications for Aβ cytotoxicity, which may occur through the ability of oligomers to form abnormal water and ion channels in cell membranes.
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Affiliation(s)
- S. R. Natesh
- Biological Sciences Collegiate Division, The University of Chicago, Chicago, Illinois 60637, USA
| | - A. R. Hummels
- Biological Sciences Collegiate Division, The University of Chicago, Chicago, Illinois 60637, USA
| | - J. R. Sachleben
- Division of Biological Sciences, The University of Chicago, Chicago, Illinois 60637, USA
| | - T. R. Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - K. F. Freed
- James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - J. F. Douglas
- Material Measurement Laboratory, Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - S. C. Meredith
- Departments of Pathology, Biochemistry, and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - E. J. Haddadian
- Biological Sciences Collegiate Division, The University of Chicago, Chicago, Illinois 60637, USA
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5
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Yang Y, Jalali S, Nilsson BL, Dias CL. Binding Mechanisms of Amyloid-like Peptides to Lipid Bilayers and Effects of Divalent Cations. ACS Chem Neurosci 2021; 12:2027-2035. [PMID: 33973758 DOI: 10.1021/acschemneuro.1c00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In several neurodegenerative diseases, cell toxicity can emerge from damage produced by amyloid aggregates to lipid membranes. The details accounting for this damage are poorly understood including how individual amyloid peptides interact with phospholipid membranes before aggregation. Here, we use all-atom molecular dynamics simulations to investigate the molecular mechanisms accounting for amyloid-membrane interactions and the role played by calcium ions in this interaction. Model peptides known to self-assemble into amyloid fibrils and bilayer made from zwitterionic and anionic lipids are used in this study. We find that both electrostatic and hydrophobic interactions contribute to peptide-bilayer binding. In particular, the attraction of peptides to lipid bilayers is dominated by electrostatic interactions between positive residues and negative phosphate moieties of lipid head groups. This attraction is stronger for anionic bilayers than for zwitterionic ones. Hydrophobicity drives the burial of nonpolar residues into the interior of the bilayer producing strong binding in our simulations. Moreover, we observe that the attraction of peptides to the bilayer is significantly reduced in the presence of calcium ions. This is due to the binding of calcium ions to negative phosphate moieties of lipid head groups, which leaves phospholipid bilayers with a net positive charge. Strong binding of the peptide to the membrane occurs less frequently in the presence of calcium ions and involves the formation of a "Ca2+ bridge".
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Bradley L. Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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6
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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: 368] [Impact Index Per Article: 122.7] [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.
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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
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7
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Liu Y, Zhang D, Zhang Y, Tang Y, Xu L, He H, Wu J, Zheng J. Molecular Dynamics Simulations of Cholesterol Effects on the Interaction of hIAPP with Lipid Bilayer. J Phys Chem B 2020; 124:7830-7841. [DOI: 10.1021/acs.jpcb.0c05742] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yonglan Liu
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Lijian Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Huacheng He
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Jiang Wu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P. R. China
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
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8
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Lu Y, Shi XF, Nguyen PH, Sterpone F, Salsbury FR, Derreumaux P. Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. J Phys Chem B 2019; 123:2687-2696. [PMID: 30813725 DOI: 10.1021/acs.jpcb.9b00431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The omega-3 and omega-6 polyunsaturated fatty acids are two important components of cell membranes in human brains. When incorporated into phospholipids, omega-3 slows the progression of Alzheimer's disease (AD), whereas omega-6 is linked to increased risk of AD. Little is known on the amyloid-β (Aβ) conformations in membranes rich in omega-3 and omega-6 phospholipids. Herein, the structural properties of the Aβ29-42 dimer embedded in both fatty acid membranes were comparatively studied to a 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) bilayer using all-atom molecular dynamics (MD) simulations. Starting from α-helix, both omega-6 and omega-3 membranes promote new orientations and conformations of the dimer, in agreement with the observed dependence of Aβ production upon addition of these two fatty acids. This conformational result is corroborated by atomistic MD simulations of the dimer of the 99 amino acid C-terminal fragment of amyloid precursor protein spanning the residues 15-55. Starting from β-sheet, omega-6 membrane promotes helical and disordered structures of Aβ29-42 dimer, whereas omega-3 membrane preserves the β-sheet structures differing however from those observed in POPC. Remarkably, the mixture of the two fatty acids and POPC depicts another conformational ensemble of the Aβ29-42 dimer. This finding demonstrates that variation in the abundance of the molecular phospholipids, which changes with age, modulates membrane-embedded Aβ oligomerization.
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Affiliation(s)
- Yan Lu
- School of Physics and Optoelectronic Engineering , Xidian University , Xi'an 710071 , China
| | - Xiao-Feng Shi
- School of Physics and Optoelectronic Engineering , Xidian University , Xi'an 710071 , China
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS , Université Paris Diderot, Sorbonne Paris Cite , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS , Université Paris Diderot, Sorbonne Paris Cite , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Freddie R Salsbury
- Department of Physics , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,Faculty of Pharmacy , Ton Duc Thang University , Ho Chi Minh City , Vietnam
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9
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Liu Y, Ren B, Zhang Y, Sun Y, Chang Y, Liang G, Xu L, Zheng J. Molecular simulation aspects of amyloid peptides at membrane interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1906-1916. [PMID: 29421626 DOI: 10.1016/j.bbamem.2018.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022]
Abstract
The interactions of amyloid peptides with cell membranes play an important role in maintaining the integrity and functionality of cell membrane. A thorough molecular-level understanding of the structure, dynamics, and interactions between amyloid peptides and cell membranes is critical to amyloid aggregation and toxicity mechanisms for the bench-to-bedside applications. Here we review the most recent computational studies of amyloid peptides at model cell membranes. Different mechanisms of action of amyloid peptides on/in cell membranes, targeted by different computational techniques at different lengthscales and timescales, are rationally discussed. Finally, we have proposed some new insights into the remaining challenges and perspectives for future studies to improve our understanding of the activity of amyloid peptides associated with protein-misfolding diseases. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Yonglan Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yanxian Zhang
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yung Chang
- R&D Center for Membrane Technology and Department of Chemical EngineeringChung Yuan Christian University, Chung-Li, Taoyuan 320, Taiwan
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing 400044, PR China
| | - Lijian Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, College of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, PR China; Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH 44325, United States.
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10
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De Santis A, La Manna S, Krauss IR, Malfitano AM, Novellino E, Federici L, De Cola A, Di Matteo A, D'Errico G, Marasco D. Nucleophosmin-1 regions associated with acute myeloid leukemia interact differently with lipid membranes. Biochim Biophys Acta Gen Subj 2018; 1862:967-978. [PMID: 29330024 DOI: 10.1016/j.bbagen.2018.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/04/2017] [Accepted: 01/08/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Augusta De Santis
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Anna Maria Malfitano
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Luca Federici
- Department of Medical, Oral and Biotechnological Sciences and CeSI-MeT, University of Chieti "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Antonella De Cola
- Department of Medical, Oral and Biotechnological Sciences and CeSI-MeT, University of Chieti "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gerardino D'Errico
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy.
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11
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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12
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Zhang M, Hu R, Ren B, Chen H, Jiang B, Ma J, Zheng J. Molecular Understanding of Aβ-hIAPP Cross-Seeding Assemblies on Lipid Membranes. ACS Chem Neurosci 2017; 8:524-537. [PMID: 27936589 DOI: 10.1021/acschemneuro.6b00247] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Amyloid-β (Aβ) and human islet polypeptide (hIAPP) are the causative agents responsible for Alzheimer's disease (AD) and type II diabetes (T2D), respectively. While numerous studies have reported the cross-seeding behavior of Aβ and hIAPP in solution, little effort has been made to examine the cross-seeding of Aβ and hIAPP in the presence of cell membranes, which is more biologically relevant to the pathological link between AD and T2D. In this work, we computationally study the cross-seeding and adsorption behaviors of Aβ and hIAPP on zwitterionic POPC and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG) mixed bilayers using all-atom molecular dynamics (MD) simulations, particularly aiming to the effects of the initial orientation of the Aβ-hIAPP assembly and the lipid composition of cell membranes on mutual structural and interaction changes in both Aβ-hIAPP assembly and lipid bilayers at the atomic level. Aβ-hIAPP cross-seeding assembly always preferred to adopt a specific orientation and interface to associate with both lipid bilayers strongly via the N-terminal strands of Aβ. Such membrane-bound orientation explains experimental observation that hybrid Aβ-hIAPP fibrils on cell membranes showed similar morphologies to pure hIAPP fibrils. Moreover, Aβ-hIAPP assembly, regardless of its initial orientations, interacted more strongly with POPC/POPG bilayer than POPC bilayer, indicating that electrostatic interactions are the major forces governing peptide-lipid interactions. Strong electrostatic interactions were also attributed to the formation of Ca2+ bridges connecting both negatively charged Glu of Aβ and PO4 head groups of lipids, which facilitate the association of Aβ-hIAPP with the POPC/POPG bilayer. It was also found that the strong peptide-lipid binding reduced lipid fluidity. Both facts imply that Aβ-hIAPP assembly may induce cell damage by altering calcium homeostasis and cell membrane phase. This work provides a better fundamental understanding of cross-seeding of Aβ and hIAPP on cell membranes and a potential pathological link between AD and T2D.
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Affiliation(s)
- Mingzhen Zhang
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Rundong Hu
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Baiping Ren
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Hong Chen
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Binbo Jiang
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- College
of Chemical and Biological Engineering Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Jie Ma
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
- State
Key Laboratory of Pollution Control and Resource Reuse School of Environmental
Science and Engineering, Tongji University, Shanghai 200092, China
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
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13
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Korshavn KJ, Satriano C, Lin Y, Zhang R, Dulchavsky M, Bhunia A, Ivanova MI, Lee YH, La Rosa C, Lim MH, Ramamoorthy A. Reduced Lipid Bilayer Thickness Regulates the Aggregation and Cytotoxicity of Amyloid-β. J Biol Chem 2017; 292:4638-4650. [PMID: 28154182 DOI: 10.1074/jbc.m116.764092] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/31/2017] [Indexed: 11/06/2022] Open
Abstract
The aggregation of amyloid-β (Aβ) on lipid bilayers has been implicated as a mechanism by which Aβ exerts its toxicity in Alzheimer's disease (AD). Lipid bilayer thinning has been observed during both oxidative stress and protein aggregation in AD, but whether these pathological modifications of the bilayer correlate with Aβ misfolding is unclear. Here, we studied peptide-lipid interactions in synthetic bilayers of the short-chain lipid dilauroyl phosphatidylcholine (DLPC) as a simplified model for diseased bilayers to determine their impact on Aβ aggregate, protofibril, and fibril formation. Aβ aggregation and fibril formation in membranes composed of dioleoyl phosphatidylcholine (DOPC) or 1- palmitoyl-2-oleoyl phosphatidylcholine mimicking normal bilayers served as controls. Differences in aggregate formation and stability were monitored by a combination of thioflavin-T fluorescence, circular dichroism, atomic force microscopy, transmission electron microscopy, and NMR. Despite the ability of all three lipid bilayers to catalyze aggregation, DLPC accelerates aggregation at much lower concentrations and prevents the fibrillation of Aβ at low micromolar concentrations. DLPC stabilized globular, membrane-associated oligomers, which could disrupt the bilayer integrity. DLPC bilayers also remodeled preformed amyloid fibrils into a pseudo-unfolded, molten globule state, which resembled on-pathway, protofibrillar aggregates. Whereas the stabilized, membrane-associated oligomers were found to be nontoxic, the remodeled species displayed toxicity similar to that of conventionally prepared aggregates. These results provide mechanistic insights into the roles that pathologically thin bilayers may play in Aβ aggregation on neuronal bilayers, and pathological lipid oxidation may contribute to Aβ misfolding.
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Affiliation(s)
- Kyle J Korshavn
- From the Department of Chemistry.,Program in Biophysics, and
| | - Cristina Satriano
- the Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Yuxi Lin
- the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - Mark Dulchavsky
- Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Anirban Bhunia
- the Department of Biophysics, Bose Institute, Kolkata 700009, India, and
| | - Magdalena I Ivanova
- Program in Biophysics, and.,Department of Neurology, University of Michigan, Ann Arbor, Michigan 48109
| | - Young-Ho Lee
- the Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Carmelo La Rosa
- the Department of Chemical Sciences, University of Catania, Catania 95124, Italy
| | - Mi Hee Lim
- the Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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14
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Zhang M, Ren B, Chen H, Sun Y, Ma J, Jiang B, Zheng J. Molecular Simulations of Amyloid Structures, Toxicity, and Inhibition. Isr J Chem 2016. [DOI: 10.1002/ijch.201600075] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Mingzhen Zhang
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Baiping Ren
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Hong Chen
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology Tianjin University Tianjin 300072 P. R. China
| | - Jie Ma
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
- State Key Laboratory of Pollution Control and Resource Reuse School of Environmental Science and Engineering Tongji University Shanghai 200092 P. R. China
| | - Binbo Jiang
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
- College of Chemical and Biological Engineering Zhejiang University Hangzhou Zhejiang 310027 P. R. China
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA
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