1
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John T, Rampioni A, Poger D, Mark AE. Molecular Insights into the Dynamics of Amyloid Fibril Growth: Elongation and Lateral Assembly of GNNQQNY Protofibrils. ACS Chem Neurosci 2024; 15:716-723. [PMID: 38235697 DOI: 10.1021/acschemneuro.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Abstract
The self-assembly of peptides and proteins into β-sheet rich amyloid fibrils is linked to both functional and pathological states. In this study, the growth of fibrillar structures of the short peptide GNNQQNY, a fragment from the yeast prion Sup35 protein, was examined. Molecular dynamics simulations were used to study alternative mechanisms of fibril growth, including elongation through binding of monomers as well as fibril self-assembly into larger, more mature structures. It was found that after binding, monomers diffused along preformed fibrils toward the ends, supporting the mechanism of fibril growth via elongation. Lateral assembly of protofibrils was found to occur readily, suggesting that this could be the key to transitioning from isolated fibrils to mature multilayer structures. Overall, the work provides mechanistic insights into the competitive pathways that govern amyloid fibril growth.
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Affiliation(s)
- Torsten John
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Aldo Rampioni
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
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2
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Nandi S, Sarkar N. Interactions between Lipid Vesicle Membranes and Single Amino Acid Fibrils: Probable Origin of Specific Neurological Disorders. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1971-1987. [PMID: 38240221 DOI: 10.1021/acs.langmuir.3c02429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Amyloid fibrils are known to be responsible for several neurological disorders, like Alzheimer's disease (AD), Parkinson's disease (PD), etc. For decades, mostly proteins and peptide-based amyloid fibrils have been focused on, and the topic has acknowledged the rise, development, understanding of, and controversy, as well. However, the single amino acid based amyloid fibrils, responsible for several disorders, such as phenylketonuria, tyrosenimia type II, hypermethioninemia, etc., have gotten scientific attention lately. To understand the molecular level pathogenesis of such disorders originated due to the accumulation of single amino acid-based amyloid fibrils, interaction of these fibrils with phospholipid vesicle membranes is found to be an excellent cell-free in vitro setup. Based on such an in vitro setup, these fibrils show a generic mechanism of membrane insertion driven by electrostatic and hydrophobic effects inside the membrane that reduces the integral rigidity of the membrane. Alteration of such fundamental properties of the membrane, therefore, might be referred to as one of the prime pathological factors for the development of these neurological disorders. Hence, such interactions must be investigated in cellular and intracellular compartments to design suitable therapeutic modulators against fibrils.
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Affiliation(s)
- Sourav Nandi
- Yale School of Medicine, Yale University, New Haven, Connecticut 06510, United States
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, 721302, West Bengal, India
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3
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Yokoyama K, Barbour E, Hirschkind R, Martinez Hernandez B, Hausrath K, Lam T. Protein Corona Formation and Aggregation of Amyloid β 1-40-Coated Gold Nanocolloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:1728-1746. [PMID: 38194428 DOI: 10.1021/acs.langmuir.3c02923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Amyloid fibrillogenesis is a pathogenic protein aggregation process that occurs through a highly ordered process of protein-protein interactions. To better understand the protein-protein interactions involved in amyloid fibril formation, we formed nanogold colloid aggregates by stepwise additions of ∼2 nmol of amyloid β 1-40 peptide (Aβ1-40) at pH ∼3.7 and ∼25 °C. The processes of protein corona formation and building of gold colloid [diameters (d) of 20 and 80 nm] aggregates were confirmed by a red-shift of the surface plasmon resonance (SPR) band, λpeak, as the number of Aβ1-40 peptides [N(Aβ1-40)] increased. The normalized red-shift of λpeak, Δλ, was correlated with the degree of protein aggregation, and this process was approximated as the adsorption isotherm explained by the Langmuir-Freundlich model. As the coverage fraction (θ) was analyzed as a function of ϕ, which is the N(Aβ1-40) per total surface area of nanogold colloids available for adsorption, the parameters for explaining the Langmuir-Freundlich model were in good agreement for both 20 and 80 nm gold, indicating that ϕ could define the stage of the aggregation process. Surface-enhanced Raman scattering (SERS) imaging was conducted at designated values of ϕ and suggested that a protein-gold surface interaction during the initial adsorption stage may be dependent on the nanosize. The 20 nm gold case seems to prefer a relatively smaller contacting section, such as a -C-N or C═C bond, but a plane of the benzene ring may play a significant role for 80 nm gold. Regardless of the size of the particles, the β-sheet and random coil conformations were considered to be used to form gold colloid aggregates. The methodology developed in this study allows for new insights into protein-protein interactions at distinct stages of aggregation.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Eli Barbour
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Rachel Hirschkind
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Bryan Martinez Hernandez
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Kaylee Hausrath
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
| | - Theresa Lam
- Department of Chemistry, The State University of New York Geneseo College, 1 College Circle, Geneseo, New York 14454, United States
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4
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Abstract
It is known that oligomers of amyloid-β (Aβ) peptide are associated with Alzheimer's disease. Aβ has two isoforms: Aβ40 and Aβ42. Although the difference between Aβ40 and Aβ42 is only two additional C-terminal residues, Aβ42 aggregates much faster than Aβ40. It is unknown what role the C-terminal two residues play in accelerating aggregation. Since Aβ42 is more toxic than Aβ40, its oligomerization process needs to be clarified. Moreover, clarifying the differences between the oligomerization processes of Aβ40 and Aβ42 is essential to elucidate the key factors of oligomerization. Therefore, to investigate the dimerization process, which is the early oligomerization process, Hamiltonian replica-permutation molecular dynamics simulations were performed for Aβ40 and Aβ42. We identified a key residue, Arg5, for the Aβ42 dimerization. The two additional residues in Aβ42 allow the C-terminus to form contact with Arg5 because of the electrostatic attraction between them, and this contact stabilizes the β-hairpin. This β-hairpin promotes dimer formation through the intermolecular β-bridges. Thus, we examined the effects of amino acid substitutions of Arg5, thereby confirming that the mutations remarkably suppressed the aggregation of Aβ42. Moreover, the mutations of Arg5 suppressed the Aβ40 aggregation. It was found by analyzing the simulations that Arg5 is important for Aβ40 to form intermolecular contacts. Thus, it was clarified that the role of Arg5 in the oligomerization process varies due to the two additional C-terminal residues.
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Affiliation(s)
- Satoru
G. Itoh
- Institute
for Molecular Science, National Institutes
of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Department
of Structural Molecular Science, SOKENDAI
(The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Maho Yagi-Utsumi
- Institute
for Molecular Science, National Institutes
of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Department
of Functional Molecular Science, SOKENDAI
(The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan,Graduate
School of Pharmaceutical Sciences, Nagoya
City University, Nagoya, Aichi 465-8603, Japan
| | - Koichi Kato
- Institute
for Molecular Science, National Institutes
of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Department
of Functional Molecular Science, SOKENDAI
(The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan,Graduate
School of Pharmaceutical Sciences, Nagoya
City University, Nagoya, Aichi 465-8603, Japan
| | - Hisashi Okumura
- Institute
for Molecular Science, National Institutes
of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Exploratory
Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan,Department
of Structural Molecular Science, SOKENDAI
(The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan,
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5
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Ilie IM, Bacci M, Vitalis A, Caflisch A. Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophys J 2022; 121:2813-2825. [PMID: 35672948 DOI: 10.1016/j.bpj.2022.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/20/2022] [Accepted: 06/01/2022] [Indexed: 11/18/2022] Open
Abstract
Misfolding of the cellular prion protein (PrPC) is associated with lethal neurodegeneration. PrPC consists of a flexible tail (residues 23-123) and a globular domain (residues 124-231) whose C-terminal end is anchored to the cell membrane. The neurotoxic antibody POM1 and the innocuous antibody POM6 recognize the globular domain. Experimental evidence indicates that POM1 binding to PrPC emulates the influence on PrPC of the misfolded prion protein (PrPSc) while the binding of POM6 has the opposite biological response. Little is known about the potential interactions between flexible tail, globular domain, and the membrane. Here, we used atomistic simulations to investigate how these interactions are modulated by the binding of the Fab fragments of POM1 and POM6 to PrPC and by interstitial sequence truncations to the flexible tail. The simulations show that the binding of the antibodies restricts the range of orientations of the globular domain with respect to the membrane and decreases the distance between tail and membrane. Five of the six sequence truncations influence only marginally this distance and the contact patterns between tail and globular domain. The only exception is a truncation coupled to a charge inversion mutation of four N-terminal residues, which increases the distance of the flexible tail from the membrane. The interactions of the flexible tail and globular domain are modulated differently by the two antibodies.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Marco Bacci
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich, Switzerland.
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6
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Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation. Molecules 2022; 27:molecules27082483. [PMID: 35458686 PMCID: PMC9030874 DOI: 10.3390/molecules27082483] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 01/02/2023] Open
Abstract
Alzheimer’s disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) simulation studies of Aβ peptides and Aβ fragments on their aggregation, aggregation inhibition, amyloid fibril conformations in equilibrium, and disruption of the amyloid fibril by ultrasonic wave and infrared laser irradiation. In the aggregation of Aβ, a β-hairpin structure promotes the formation of intermolecular β-sheet structures. Aβ peptides tend to exist at hydrophilic/hydrophobic interfaces and form more β-hairpin structures than in bulk water. These facts are the reasons why the aggregation is accelerated at the interface. We also explain how polyphenols, which are attracting attention as aggregation inhibitors of Aβ peptides, interact with Aβ. An MD simulation study of the Aβ amyloid fibrils in equilibrium is also presented: the Aβ amyloid fibril has a different structure at one end from that at the other end. The amyloid fibrils can be destroyed by ultrasonic wave and infrared laser irradiation. The molecular mechanisms of these amyloid fibril disruptions are also explained, particularly focusing on the function of water molecules. Finally, we discuss the prospects for developing treatments for Alzheimer’s disease using MD simulations.
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7
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Watanabe-Nakayama T, Ono K. Single-molecule Observation of Self-Propagating Amyloid Fibrils. Microscopy (Oxf) 2022; 71:133-141. [DOI: 10.1093/jmicro/dfac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
The assembly of misfolded proteins into amyloid fibrils is associated with amyloidosis, including neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, and prion diseases. The self-propagation of amyloid fibrils is widely observed in the aggregation pathways of numerous amyloidogenic proteins. This propensity with plasticity in primary nucleation allows amyloid fibril polymorphism, which is correlated with the pathology/phenotypes of patients. Because the interference with the nucleation and replication processes of amyloid fibrils can alter the amyloid structure and the outcome of the disease, these processes can be a target for developing clinical drugs. Single-molecule observation of amyloid fibril replication can be an experimental system to provide the kinetic parameters for simulation studies and confirm the effect of clinical drugs. Here, we review single-molecule observation of the amyloid fibril replication process using fluorescence microscopy and time-lapse atomic force microscopy, including high-speed atomic force microscopy. We discussed the amyloid fibril replication process and combined single-molecule observation results with molecular dynamics simulations.
Mini Abstract Structural dynamics in amyloid aggregation is related with various Alzheimer’s and Parkinson’s disease symptoms. Single-molecule observation using high-speed atomic force microscopy can directly visualize the structural dynamics of individual amyloid aggregate assemblies. Here, we review historical and recent studies of single-molecule observation of amyloid aggregation with supportive molecular dynamics simulation.
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Affiliation(s)
| | - Kenjiro Ono
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa University, 13-1, Takara-machi, Kanazawa 920-8640, Japan
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8
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Tachi Y, Itoh SG, Okumura H. Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments. Biophys Physicobiol 2022; 19:1-18. [PMID: 35666692 PMCID: PMC9135617 DOI: 10.2142/biophysico.bppb-v19.0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Yuhei Tachi
- Department of Physics, Graduate school of Science, Nagoya University
| | - Satoru G. Itoh
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
| | - Hisashi Okumura
- Institute for Molecular Science, National Institutes of Natural Sciences
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9
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He H, Xu J, Li C, Gao T, Jiang P, Jiang F, Liu Y. Insights into Mechanism of Aβ 42 Fibril Growth on Surface of Graphene Oxides: Oxidative Degree Matters. Adv Healthc Mater 2021; 10:e2100436. [PMID: 34050633 DOI: 10.1002/adhm.202100436] [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: 03/16/2021] [Revised: 05/19/2021] [Indexed: 01/30/2023]
Abstract
The filamentous β-amyloid deposition has been regarded as the hallmark pathology of Alzheimer's disease (AD). Nanomaterials such as graphene oxides (GOs) have achieved significant progress in the therapy of AD, but the molecular pathway of the growth propagation remains challenging to investigate, especially on the surfaces of materials. The thermodynamics and kinetics of fibril elongation on GO surfaces with different oxidative degrees have been investigated by a combination of in vitro experiments and simulations. ThT kinetics, calorimetric measurements, and TEM observations suggest that low oxidative GO-10 promotes the fibril elongation, while both high oxidative GO-20 and GO-40 inhibit the fibril elongation. Computational results reveal that the apparent regulation behaviors of GOs on filament growth depend on the balance between the promoting effect by templating the incoming of monomers and the retarding effect by capturing the monomer during docking and locking phases through hydrogen bonding. This work will promote the understanding of the interplay between biomolecules and materials, thus providing new thoughts for the rational design of novel materials for amyloidosis therapy.
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Affiliation(s)
- Huan He
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province College of Chemistry and Chemical Engineering Institute of Advanced Materials and Nanotechnology Wuhan University of Science and Technology Wuhan 430081 P. R. China
| | - Juan Xu
- Key Laboratory of Chemistry & Sauvage Center for Molecular Sciences College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 P. R. China
- College of Chemistry and Chemical Engineering Hubei Polytechnic University Huangshi 435003 P. R. China
| | - Chen‐Qiao Li
- Key Laboratory of Chemistry & Sauvage Center for Molecular Sciences College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 P. R. China
| | - Tian Gao
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province College of Chemistry and Chemical Engineering Institute of Advanced Materials and Nanotechnology Wuhan University of Science and Technology Wuhan 430081 P. R. China
| | - Peng Jiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) School of Pharmaceutical Sciences Wuhan University Wuhan 430071 P. R. China
| | - Feng‐Lei Jiang
- Key Laboratory of Chemistry & Sauvage Center for Molecular Sciences College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 P. R. China
| | - Yi Liu
- Key Laboratory of Coal Conversion and New Carbon Materials of Hubei Province College of Chemistry and Chemical Engineering Institute of Advanced Materials and Nanotechnology Wuhan University of Science and Technology Wuhan 430081 P. R. China
- Key Laboratory of Chemistry & Sauvage Center for Molecular Sciences College of Chemistry and Molecular Sciences Wuhan University Wuhan 430072 P. R. China
- Key Laboratory of Separation Membranes and Membrane Process School of Chemistry and Chemical Engineering & College of Environmental Science and Engineering Tiangong University Tianjin 300387 P. R. China
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10
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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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11
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Multiscale Models for Fibril Formation: Rare Events Methods, Microkinetic Models, and Population Balances. Life (Basel) 2021; 11:life11060570. [PMID: 34204410 PMCID: PMC8234428 DOI: 10.3390/life11060570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/30/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022] Open
Abstract
Amyloid fibrils are thought to grow by a two-step dock-lock mechanism. However, previous simulations of fibril formation (i) overlook the bi-molecular nature of the docking step and obtain rates with first-order units, or (ii) superimpose the docked and locked states when computing the potential of mean force for association and thereby muddle the docking and locking steps. Here, we developed a simple microkinetic model with separate locking and docking steps and with the appropriate concentration dependences for each step. We constructed a simple model comprised of chiral dumbbells that retains qualitative aspects of fibril formation. We used rare events methods to predict separate docking and locking rate constants for the model. The rate constants were embedded in the microkinetic model, with the microkinetic model embedded in a population balance model for “bottom-up” multiscale fibril growth rate predictions. These were compared to “top-down” results using simulation data with the same model and multiscale framework to obtain maximum likelihood estimates of the separate lock and dock rate constants. We used the same procedures to extract separate docking and locking rate constants from experimental fibril growth data. Our multiscale strategy, embedding rate theories, and kinetic models in conservation laws should help to extract docking and locking rate constants from experimental data or long molecular simulations with correct units and without compromising the molecular description.
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12
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Okumura H, Itoh SG, Nakamura K, Kawasaki T. Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations. J Phys Chem B 2021; 125:4964-4976. [PMID: 33961416 DOI: 10.1021/acs.jpcb.0c11491] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Water plays a crucial role in the formation and destruction of biomolecular structures. The mechanism for destroying biomolecular structures was thought to be an active breaking of hydrogen bonds by water molecules. However, using nonequilibrium molecular dynamics simulations, in which an amyloid-β amyloid fibril was destroyed via infrared free-electron laser (IR-FEL) irradiation, we discovered a new mechanism, in which water molecules disrupt protein aggregates. The intermolecular hydrogen bonds formed by C═O and N-H in the fibril are broken at each pulse of laser irradiation. These bonds spontaneously re-form after the irradiation in many cases. However, when a water molecule happens to enter the gap between C═O and N-H, it inhibits the re-formation of the hydrogen bonds. Such sites become defects in the regularly aligned hydrogen bonds, from which all hydrogen bonds in the intermolecular β-sheet are broken as the fraying spreads. This role of water molecules is entirely different from other known mechanisms. This new mechanism can explain the recent experiments showing that the amyloid fibrils are not destroyed by laser irradiation under dry conditions. Additionally, we found that helix structures form more after the amyloid disruption; this is because the resonance frequency is different in a helix structure. Our findings provide a theoretical basis for the application of IR-FEL to the future treatment of amyloidosis.
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Affiliation(s)
- Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Satoru G Itoh
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.,Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Kazuhiro Nakamura
- Department of Laboratory Sciences, Graduate School of Health Sciences, Gunma University, Maebashi, Gunma 371-8514, Japan
| | - Takayasu Kawasaki
- IR Free Electron Laser Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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13
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Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies. Int J Mol Sci 2021; 22:ijms22041859. [PMID: 33668406 PMCID: PMC7918115 DOI: 10.3390/ijms22041859] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/06/2023] Open
Abstract
Aggregates of amyloid-β (Aβ) peptides are known to be related to Alzheimer’s disease. Their aggregation is enhanced at hydrophilic–hydrophobic interfaces, such as a cell membrane surface and air-water interface, and is inhibited by polyphenols, such as myricetin and rosmarinic acid. We review molecular dynamics (MD) simulation approaches of a full-length Aβ peptide, Aβ40, and Aβ(16–22) fragments in these environments. Since these peptides have both hydrophilic and hydrophobic amino acid residues, they tend to exist at the interfaces. The high concentration of the peptides accelerates the aggregation there. In addition, Aβ40 forms a β-hairpin structure, and this structure accelerates the aggregation. We also describe the inhibition mechanism of the Aβ(16–22) aggregation by polyphenols. The aggregation of Aβ(16–22) fragments is caused mainly by the electrostatic attraction between charged amino acid residues known as Lys16 and Glu22. Since polyphenols form hydrogen bonds between their hydroxy and carboxyl groups and these charged amino acid residues, they inhibit the aggregation.
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14
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Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins. Proc Natl Acad Sci U S A 2020; 117:28775-28783. [PMID: 33148805 PMCID: PMC7682573 DOI: 10.1073/pnas.1920455117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although folded proteins are commonly depicted as simplistic combinations of β-strands and α-helices, the actual properties and functions of these secondary-structure elements in their native contexts are just partly understood. The principal reason is that the behavior of individual β- and α-elements is obscured by the global folding cooperativity. In this study, we have circumvented this problem by designing frustrated variants of the mixed α/β-protein S6, which allow the structural behavior of individual β-strands and α-helices to be targeted selectively by stopped-flow kinetics, X-ray crystallography, and solution-state NMR. Essentially, our approach is based on provoking intramolecular "domain swap." The results show that the α- and β-elements have quite different characteristics: The swaps of β-strands proceed via global unfolding, whereas the α-helices are free to swap locally in the native basin. Moreover, the α-helices tend to hybridize and to promote protein association by gliding over to neighboring molecules. This difference in structural behavior follows directly from hydrogen-bonding restrictions and suggests that the protein secondary structure defines not only tertiary geometry, but also maintains control in function and structural evolution. Finally, our alternative approach to protein folding and native-state dynamics presents a generally applicable strategy for in silico design of protein models that are computationally testable in the microsecond-millisecond regime.
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15
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Sasanian N, Bernson D, Horvath I, Wittung-Stafshede P, Esbjörner EK. Redox-Dependent Copper Ion Modulation of Amyloid-β (1-42) Aggregation In Vitro. Biomolecules 2020; 10:E924. [PMID: 32570820 PMCID: PMC7355640 DOI: 10.3390/biom10060924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 12/20/2022] Open
Abstract
Plaque deposits composed of amyloid-β (Aβ) fibrils are pathological hallmarks of Alzheimer's disease (AD). Although copper ion dyshomeostasis is apparent in AD brains and copper ions are found co-deposited with Aβ peptides in patients' plaques, the molecular effects of copper ion interactions and redox-state dependence on Aβ aggregation remain elusive. By combining biophysical and theoretical approaches, we here show that Cu2+ (oxidized) and Cu+ (reduced) ions have opposite effects on the assembly kinetics of recombinant Aβ(1-42) into amyloid fibrils in vitro. Cu2+ inhibits both the unseeded and seeded aggregation of Aβ(1-42) at pH 8.0. Using mathematical models to fit the kinetic data, we find that Cu2+ prevents fibril elongation. The Cu2+-mediated inhibition of Aβ aggregation shows the largest effect around pH 6.0 but is lost at pH 5.0, which corresponds to the pH in lysosomes. In contrast to Cu2+, Cu+ ion binding mildly catalyzes the Aβ(1-42) aggregation via a mechanism that accelerates primary nucleation, possibly via the formation of Cu+-bridged Aβ(1-42) dimers. Taken together, our study emphasizes redox-dependent copper ion effects on Aβ(1-42) aggregation and thereby provides further knowledge of putative copper-dependent mechanisms resulting in AD.
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Affiliation(s)
| | | | | | | | - Elin K. Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (N.S.); (D.B.); (I.H.); (P.W.-S.)
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16
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Frigori RB, Barroso da Silva FL, Carvalho PPD, Alves NA. Occurrence of Biased Conformations as Precursors of Assembly States in Fibril Elongation of Amyloid-β Fibril Variants: An In Silico Study. J Phys Chem B 2020; 124:2798-2805. [DOI: 10.1021/acs.jpcb.0c01360] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rafael B. Frigori
- Universidade Tecnológica Federal do Paraná, Rua Cristo Rei 19, Toledo 85902-490, Paraná, Brazil
| | - Fernando L. Barroso da Silva
- Departamento de Ciências Biomoleculares, FCFRP, Universidade de São Paulo, Avenida do Café, s/no, Ribeirão Preto 14040-903, São Paulo, Brazil
| | - Patrícia P. D. Carvalho
- Departamento de Fı́sica, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto 14040-901, São Paulo, Brazil
| | - Nelson A. Alves
- Departamento de Fı́sica, FFCLRP, Universidade de São Paulo, Avenida Bandeirantes, 3900, Ribeirão Preto 14040-901, São Paulo, Brazil
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17
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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18
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Computational studies of protein aggregation mediated by amyloid: Fibril elongation and secondary nucleation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:461-504. [DOI: 10.1016/bs.pmbts.2019.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Agrawal N, Skelton AA. Structure and Function of Alzheimer’s Amyloid βeta Proteins from Monomer to Fibrils: A Mini Review. Protein J 2019; 38:425-434. [DOI: 10.1007/s10930-019-09854-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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Xu Y, Safari MS, Ma W, Schafer NP, Wolynes PG, Vekilov PG. Steady, Symmetric, and Reversible Growth and Dissolution of Individual Amyloid-β Fibrils. ACS Chem Neurosci 2019; 10:2967-2976. [PMID: 31099555 DOI: 10.1021/acschemneuro.9b00179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Oligomers and fibrils of the amyloid-β (Aβ) peptide are implicated in the pathology of Alzheimer's disease. Here, we monitor the growth of individual Aβ40 fibrils by time-resolved in situ atomic force microscopy and thereby directly measure fibril growth rates. The measured growth rates in a population of fibrils that includes both single protofilaments and bundles of filaments are independent of the fibril thickness, indicating that cooperation between adjacent protofilaments does not affect incorporation of monomers. The opposite ends of individual fibrils grow at similar rates. In contrast to the "stop-and-go" kinetics that has previously been observed for amyloid-forming peptides, growth and dissolution of the Aβ40 fibrils are relatively steady for peptide concentration of 0-10 μM. The fibrils readily dissolve in quiescent peptide-free solutions at a rate that is consistent with the microscopic reversibility of growth and dissolution. Importantly, the bimolecular rate coefficient for the association of a monomer to the fibril end is significantly smaller than the diffusion limit, implying that the transition state for incorporation of a monomer into a fibril is associated with a relatively high free energy.
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Affiliation(s)
- Yuechuan Xu
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Mohammad S. Safari
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Wenchuan Ma
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
| | - Nicholas P. Schafer
- Center for Theoretical Biological Physics, Rice University, P.O. Box 1892, MS 654, Houston, Texas 77251-1892, United States
- Department of Chemistry, Rice University, P.O. Box 1892, MS 60, Houston, Texas 77251-1892, United States
| | - Peter G. Wolynes
- Center for Theoretical Biological Physics, Rice University, P.O. Box 1892, MS 654, Houston, Texas 77251-1892, United States
- Department of Chemistry, Rice University, P.O. Box 1892, MS 60, Houston, Texas 77251-1892, United States
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, Texas 77204-4004, United States
- Department of Chemistry, University of Houston, 3585 Cullen Blvd., Houston, Texas 77204-5003, United States
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21
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Grazioli G, Yu Y, Unhelkar MH, Martin RW, Butts CT. Network-Based Classification and Modeling of Amyloid Fibrils. J Phys Chem B 2019; 123:5452-5462. [PMID: 31095387 DOI: 10.1021/acs.jpcb.9b03494] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Amyloid fibrils are locally ordered protein aggregates that self-assemble under a variety of physiological and in vitro conditions. Their formation is of fundamental interest as a physical chemistry problem and plays a central role in Alzheimer's disease, Type II diabetes, and other human diseases. As the number of known amyloid fibril structures has grown, the need has arisen for a nomenclature for describing and classifying fibril types, as well as a theoretical description of the physics that gives rise to the self-assembly of these structures. Here, we introduce a systematic nomenclature and coarse-graining methodology for describing the topology of fibrils and other protein aggregates, along with a computational methodology for simulating protein aggregation. Both have mathematical underpinnings in graph theory and statistical mechanics and are consistent with available experimental data on the fibril structure and aggregation kinetics. Our graph representation of the fibril topology enables us to define a network Hamiltonian based on connectivity patterns among monomers rather than detailed intermolecular interactions, greatly speeding up the simulation of large ensembles. Our simulation strategy is capable of recapitulating the formation of all currently known amyloid fibril topologies found in the Protein Data Bank, as well as the formation kinetics of fibrils and oligomers.
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22
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Liu C, Zhao W, Xing X, Shi H, Kang B, Liu H, Li P, Ai H. An Original Monomer Sampling from a Ready‐Made Aβ
42
NMR Fibril Suggests a Turn‐β‐Strand Synergetic Seeding Mechanism. Chemphyschem 2019; 20:1649-1660. [DOI: 10.1002/cphc.201801137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Chengqiang Liu
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Wei Zhao
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Xiaofeng Xing
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Hu Shi
- School of Chemistry and Chemical EngineeringShanxi University Taiyuan 030006 China
| | - Baotao Kang
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
| | - Haiying Liu
- School of PhysicsUniversity of Jinan Jinan 250022 China
| | - Ping Li
- Key Laboratory of Life-Organic Analysis, School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165 China
| | - Hongqi Ai
- School of Chemistry and Chemical EngineeringUniversity of Jinan Jinan 250022 China
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23
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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24
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Bacci M, Caflisch A, Vitalis A. On the removal of initial state bias from simulation data. J Chem Phys 2019; 150:104105. [PMID: 30876362 DOI: 10.1063/1.5063556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Classical atomistic simulations of biomolecules play an increasingly important role in molecular life science. The structure of current computing architectures favors methods that run multiple trajectories at once without requiring extensive communication between them. Many advanced sampling strategies in the field fit this mold. These approaches often rely on an adaptive logic and create ensembles of comparatively short trajectories whose starting points are not distributed according to the correct Boltzmann weights. This type of bias is notoriously difficult to remove, and Markov state models (MSMs) are one of the few strategies available for recovering the correct kinetics and thermodynamics from these ensembles of trajectories. In this contribution, we analyze the performance of MSMs in the thermodynamic reweighting task for a hierarchical set of systems. We show that MSMs can be rigorous tools to recover the correct equilibrium distribution for systems of sufficiently low dimensionality. This is conditional upon not tampering with local flux imbalances found in the data. For a real-world application, we find that a pure likelihood-based inference of the transition matrix produces the best results. The removal of the bias is incomplete, however, and for this system, all tested MSMs are outperformed by an alternative albeit less general approach rooted in the ideas of statistical resampling. We conclude by formulating some recommendations for how to address the reweighting issue in practice.
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Affiliation(s)
- Marco Bacci
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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25
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Röder K, Joseph JA, Husic BE, Wales DJ. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800175] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Konstantin Röder
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Jerelle A. Joseph
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - Brooke E. Husic
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
| | - David J. Wales
- Department of ChemistryUniversity of CambridgeLensfield Road CB2 1EW Cambridge UK
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26
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Ilie IM, Caflisch A. Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study. J Phys Chem B 2018; 122:11072-11082. [PMID: 29965774 DOI: 10.1021/acs.jpcb.8b05236] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present a simulation study of the early events of peptide dissociation from a fibril of the Alzheimer's Aβ42 peptide. The fibril consists of layers of two adjacent Aβ42 peptides each folded in an S-shaped structure which has been determined by solid state NMR spectroscopy of a monomorphic disease-relevant species. Multiple molecular dynamics runs (16 at 310 K and 15 at 370 K) were carried out starting from an 18-peptide protofibril for a cumulative sampling of about 15 μs. The simulations show structural stability of the fibrillar core and an overall increase in the twist to about 3 degrees. The N-terminal segment 1-14 is disordered in all peptides. At both ends of the fibril, the central segment 21-29, which includes part of the β2 strand, dissociates in some of the simulations. The β1 and β3 strands, residues 15-20 and 35-41, respectively, are structurally stable. The transient binding of the N-terminal stretch to the β3 strand of the adjacent peptide at the tip is likely to contribute to the arrest phase of the stop-and-go mechanism.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry , University of Zürich , 8057 Zürich , Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry , University of Zürich , 8057 Zürich , Switzerland
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27
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Jonnalagadda SVR, Kokotidou C, Orr AA, Fotopoulou E, Henderson KJ, Choi CH, Lim WT, Choi SJ, Jeong HK, Mitraki A, Tamamis P. Computational Design of Functional Amyloid Materials with Cesium Binding, Deposition, and Capture Properties. J Phys Chem B 2018; 122:7555-7568. [DOI: 10.1021/acs.jpcb.8b04103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Chrysoula Kokotidou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
| | | | - Emmanouela Fotopoulou
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
| | | | | | - Woo Taik Lim
- Department of Applied Chemistry, Andong National University, Andong 36729, Republic of Korea
| | - Sang June Choi
- Department of Environmental Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | | | - Anna Mitraki
- Department of Materials Science and Technology, University of Crete, Heraklion 700 13, Crete, Greece
- Institute of Electronic Structure and Laser (IESL) FORTH, Heraklion 711 10, Crete, Greece
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28
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Bacci M, Langini C, Vymětal J, Caflisch A, Vitalis A. Focused conformational sampling in proteins. J Chem Phys 2018; 147:195102. [PMID: 29166086 DOI: 10.1063/1.4996879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.
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Affiliation(s)
- Marco Bacci
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Cassiano Langini
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jiří Vymětal
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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29
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Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Thermodynamics of Amyloid-β Fibril Elongation: Atomistic Details of the Transition State. ACS Chem Neurosci 2018; 9:783-789. [PMID: 29239603 PMCID: PMC5911799 DOI: 10.1021/acschemneuro.7b00409] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
Amyloid-β
(Aβ) fibrils and plaques are one of the hallmarks
of Alzheimer’s disease. While the kinetics of fibrillar growth
of Aβ have been extensively studied, several vital questions
remain. In particular, the atomistic origins of the Arrhenius barrier
observed in experiments have not been elucidated. Employing the familiar
thermodynamic integration method, we have directly simulated the dissociation
of an Aβ(15–40) (D23N mutant) peptide from
the surface of a filament along its most probable path (MPP) using
all-atom molecular dynamics. This allows for a direct calculation
of the free energy profile along the MPP, revealing a multipeak energetic
barrier between the free peptide state and the aggregated state. By
definition of the MPP, this simulated unbinding process represents
the reverse of the physical elongation pathway, allowing us to draw
biophysically relevant conclusions from the simulation data. Analyzing
the detailed atomistic interactions along the MPP, we identify the
atomistic origins of these peaks as resulting from the dock-lock mechanism
of filament elongation. Careful analysis of the dynamics of filament
elongation could prove key to the development of novel therapeutic
strategies for amyloid-related diseases.
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Affiliation(s)
- Roberto A. Rodriguez
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Liao Y. Chen
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Germán Plascencia-Villa
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - George Perry
- Department of Biology and Neurosciences Institute, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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30
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Abstract
The aggregation of the Aβ peptide (Aβ1-42) to form fibrils is a key feature of Alzheimer's disease. The mechanism is thought to be a nucleation stage followed by an elongation process. The elongation stage involves the consecutive addition of monomers to one end of the growing fibril. The aggregation process proceeds in a stop-and-go fashion and may involve off-pathway aggregates, complicating experimental and computational studies. Here we present exploration of a well-defined region in the free and potential energy landscapes for the Aβ17-42 pentamer. We find that the ideal aggregation process agrees with the previously reported dock-lock mechanism. We also analyze a large number of additional stable structures located on the multifunnel energy landscape, which constitute kinetic traps. The key contributors to the formation of such traps are misaligned strong interactions, for example the stacking of F19 and F20, as well as entropic contributions. Our results suggest that folding templates for aggregation are a necessity and that aggregation studies could employ such species to obtain a more detailed description of the process.
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Affiliation(s)
- Konstantin Röder
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
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31
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Chen J, Zha L, Hu W. Effect of solvent selectivity on crystallization-driven fibril growth kinetics of diblock copolymers. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.01.074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Cao Y, Jiang X, Han W. Self-Assembly Pathways of β-Sheet-Rich Amyloid-β(1-40) Dimers: Markov State Model Analysis on Millisecond Hybrid-Resolution Simulations. J Chem Theory Comput 2017; 13:5731-5744. [PMID: 29019683 DOI: 10.1021/acs.jctc.7b00803] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Early oligomerization during amyloid-β (Aβ) aggregation is essential for Aβ neurotoxicity. Understanding how unstructured Aβs assemble into oligomers, especially those rich in β-sheets, is essential but remains challenging as the assembly process is too transient for experimental characterization and too slow for molecular dynamics simulations. So far, atomic simulations are limited only to studies of either oligomer structures or assembly pathways for short Aβ segments. To overcome the computational challenge, we combine in this study a hybrid-resolution model and adaptive sampling techniques to perform over 2.7 ms of simulations of formation of full-length Aβ40 dimers that are the earliest toxic oligomeric species. The Markov state model is further employed to characterize the transition pathways and associated kinetics. Our results show that for two major forms of β-sheet-rich structures reported experimentally, the corresponding assembly mechanisms are markedly different. Hairpin-containing structures are formed by direct binding of soluble Aβ in β-hairpin-like conformations. Formation of parallel, in-register structures resembling fibrils occurs ∼100-fold more slowly and involves a rapid encounter of Aβ in arbitrary conformations followed by a slow structural conversion. The structural conversion proceeds via diverse pathways but always requires transient unfolding of encounter complexes. We find that the transition kinetics could be affected differently by intra-/intermolecular interactions involving individual residues in a conformation-dependent manner. In particular, the interactions involving Aβ's N-terminal part promote the assembly into hairpin-containing structures but delay the formation of fibril-like structures, thus explaining puzzling observations reported previously regarding the roles of this region in the early assembly process.
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Affiliation(s)
- Yang Cao
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Xuehan Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
| | - Wei Han
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School , Shenzhen, 518055, China
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