1
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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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2
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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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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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4
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Fukuhara D, Itoh SG, Okumura H. Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-β fragments. J Chem Phys 2022; 156:084109. [DOI: 10.1063/5.0081686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We propose the replica permutation with solute tempering (RPST) by combining the replica-permutation method (RPM) and the replica exchange with solute tempering (REST). Temperature permutations are performed among more than two replicas in RPM, whereas temperature exchanges are performed between two replicas in the replica-exchange method (REM). The temperature transition in RPM occurs more efficiently than in REM. In REST, only the temperatures of the solute region, the solute temperatures, are exchanged to reduce the number of replicas compared to REM. Therefore, RPST is expected to be an improved method taking advantage of these methods. For comparison, we applied RPST, REST, RPM, and REM to two amyloid-β(16–22) peptides in explicit water. We calculated the transition ratio and the number of tunneling events in the temperature space and the number of dimerization events of amyloid-β(16–22) peptides. The results indicate that, in RPST, the number of replicas necessary for frequent random walks in the temperature and conformational spaces is reduced compared to the other three methods. In addition, we focused on the dimerization process of amyloid-β(16–22) peptides. The RPST simulation with a relatively small number of replicas shows that the two amyloid-β(16–22) peptides form the intermolecular antiparallel β-bridges due to the hydrophilic side-chain contact between Lys and Glu and hydrophobic side-chain contact between Leu, Val, and Phe, which stabilizes the dimer of the peptides.
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Affiliation(s)
- Daiki Fukuhara
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Satoru G. Itoh
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
- 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
| | - Hisashi Okumura
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
- 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
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5
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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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6
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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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7
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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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8
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Mahmoudinobar F, Nilsson BL, Dias CL. Effects of Ions and Small Compounds on the Structure of Aβ 42 Monomers. J Phys Chem B 2021; 125:1085-1097. [PMID: 33481611 DOI: 10.1021/acs.jpcb.0c09617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aggregation of amyloid-β (Aβ) proteins in the brain is a hallmark of Alzheimer's disease. This phenomenon can be promoted or inhibited by adding small molecules to the solution where Aβ is embedded. These molecules affect the ensemble of conformations sampled by Aβ monomers even before aggregation starts. Here, we perform extensive all-atom replica exchange molecular dynamics (REMD) simulations to provide a comparative study of the ensemble of conformations sampled by Aβ42 monomers in solutions that promote (i.e., aqueous solution containing NaCl) and inhibit (i.e., aqueous solutions containing scyllo-inositol or 4-aminophenol) aggregation. Simulations performed in pure water are used as our reference. We find that secondary-structure content is only affected in an antagonistic manner by promoters and inhibitors at the C-terminus and the central hydrophilic core. Moreover, the end of the C-terminus binds more favorably to the central hydrophobic core region of Aβ42 in NaCl adopting a type of strand-loop-strand structure that is disfavored by inhibitors. Nonpolar residues that form the dry core of larger aggregates of Aβ42 (e.g., PDB ID 2BEG) are found at close proximity in these strand-loop-strand structures, suggesting that their formation could play an important role in initiating nucleation. In the presence of inhibitors, the C-terminus binds the central hydrophilic core with a higher probability than in our reference simulation. This sensitivity of the C-terminus, which is affected in an antagonistic manner by inhibitors and promoters, provides evidence for its critical role in accounting for aggregation.
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Affiliation(s)
- Farbod Mahmoudinobar
- 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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9
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Abstract
Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.
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Affiliation(s)
- C. Kokotidou
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
| | - P. Tamamis
- Texas A&M University, Artie McFerrin Department of Chemical Engineering College Station Texas 77843-3122 USA
| | - A. Mitraki
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
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10
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Zbacnik NJ, Henry CS, Manning MC. A Chemometric Approach Toward Predicting the Relative Aggregation Propensity: Aβ(1-42). J Pharm Sci 2019; 109:624-632. [PMID: 31606543 DOI: 10.1016/j.xphs.2019.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 01/19/2023]
Abstract
A number of algorithms have been developed to predict the aggregation propensity of peptides and proteins, but virtually none have the ability to provide sequence-specific information on what physicochemical properties are most important in altering aggregation propensity. In this study, a chemometric approach using reduced amino acid properties is used to examine the aggregation behavior of a highly amyloidogenic peptide, Aβ(1-42). Specific residues are identified as being critical to the aggregation process. At each of these positions, the important physicochemical properties are identified that would either accelerate or inhibit fibril formation.
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Affiliation(s)
| | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523.
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11
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Minh Thu TT, Huang SH, Tu LA, Fang ST, Li MS, Chen YC. G37V mutation of Aβ42 induces a nontoxic ellipse-like aggregate: An in vitro and in silico study. Neurochem Int 2019; 129:104512. [PMID: 31374231 DOI: 10.1016/j.neuint.2019.104512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 11/17/2022]
Abstract
The glycine zipper motif at the C-terminus of the β-amyloid (Aβ) peptide have been shown to strongly influence the formation of neurotoxic aggregates. A previous study showed that the G37L mutation dramatically reduces the Aβ toxicity in vivo and in vitro. However, the primary cause and mechanism of the glycine zipper motif on Aβ properties remain unknown. To gain molecular insights into the impact of glycine zipper on Aβ properties, we substituted the residue 37 of Glycine by Valine and studied the structural and biochemical properties of G37V mutation, Aβ42(37V), by using in vitro and in silico approaches. Unlike G37L mutation, the G37V mutation reduced toxicity substantially but did not significantly accelerate the aggregation rate or change the content of secondary structures. Further TEM analyses showed that the G37V mutation formed an ellipse-like aggregate rather than a network-like fibril as wild type or G37L mutation of Aβ42 form. This different aggregation morphology may be highly linked with the reduction of toxicity. To gain the insight for the different properties of Aβ42(37V), we studied the structure of Aβ42 and G37V mutation using the replica exchange molecular dynamics simulation. Our results demonstrate that although the overall secondary structure population is similar with Aβ42 and Aβ42(G37V), Aβ42(G37V) shows an increase in the β-turn and β-hairpin at residues 36-37 and the flexibility of the Asp23-Lys28 salt bridge. These unique structural features may be the possible reason to account for the ellipse-like morphology.
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Affiliation(s)
- Tran Thi Minh Thu
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam; Department of Applied Physics, Faculty of Applied Science, Ho Chi Minh City University of Technology - VNU HCM, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam; Department of Materials Science and Technology, University of Science-VNUHCM, 227 Nguyen Van Cu, District 5, Ho Chi Minh City, Viet Nam
| | - Shu-Hsiang Huang
- Department of Medicine, MacKay Medical College, New Taipei City, 252, Taiwan
| | - Ly Anh Tu
- Department of Applied Physics, Faculty of Applied Science, Ho Chi Minh City University of Technology - VNU HCM, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
| | - Shang-Ting Fang
- Department of Medicine, MacKay Medical College, New Taipei City, 252, Taiwan
| | - 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, Viet Nam; Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland.
| | - Yi-Cheng Chen
- Department of Medicine, MacKay Medical College, New Taipei City, 252, Taiwan.
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12
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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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13
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Shuaib S, Saini RK, Goyal D, Goyal B. Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer’s disease: key insights from molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:708-721. [DOI: 10.1080/07391102.2019.1586587] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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14
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Coskuner-Weber O. Revisiting Cu(II) Bound Amyloid-β40 and Amyloid-β42 Peptides: Varying Coordination Chemistries. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2018. [DOI: 10.18596/jotcsa.424144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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15
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Coskuner-Weber O, Uversky VN. Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int J Mol Sci 2018; 19:E336. [PMID: 29364151 PMCID: PMC5855558 DOI: 10.3390/ijms19020336] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.
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Affiliation(s)
- Orkid Coskuner-Weber
- Türkisch-Deutsche Universität, Theoretical and Computational Biophysics Group, Molecular Biotechnology, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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16
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Coskuner O, Uversky VN. Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins. J Chem Inf Model 2017; 57:1342-1358. [DOI: 10.1021/acs.jcim.6b00761] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Orkid Coskuner
- Department
of Chemistry and Neurosciences Institute, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
- Institut
für Physikalische Chemie, Universität zu Köln, Luxemburger
Strasse 116, 50939 Köln, Germany
- Molecular
Biotechnology Division, Turkisch-Deutsche Universität, Sahinkaya
Caddesi, No. 71, Beykoz, Istanbul 34820, Turkey
| | - Vladimir N. Uversky
- Department
of Molecular Medicine, USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Laboratory
of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
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17
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Linh NH, Thu TTM, Tu L, Hu CK, Li MS. Impact of Mutations at C-Terminus on Structures and Dynamics of Aβ40 and Aβ42: A Molecular Simulation Study. J Phys Chem B 2017; 121:4341-4354. [DOI: 10.1021/acs.jpcb.6b12888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nguyen Hoang Linh
- Institute for Computational Science and Technology
, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Biomedical
Engineering Department, University of Technology - VNU HCM
, 268 Ly Thuong
Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Tran Thi Minh Thu
- Institute for Computational Science and Technology
, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Biomedical
Engineering Department, University of Technology - VNU HCM
, 268 Ly Thuong
Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - LyAnh Tu
- Institute for Computational Science and Technology
, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Biomedical
Engineering Department, University of Technology - VNU HCM
, 268 Ly Thuong
Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Chin-Kun Hu
- Institute
of Physics, Academia Sinica
, 128 Academia Road Section 2, Taipei
11529, Taiwan
- National
Center for Theoretical Sciences, National Tsing Hua University
, 101 Kuang-Fu Road Section 2, Hsinch
30013, Taiwan
- Business
School, University of Shanghai for Science and Technology
, 334 Jun
Gong Road, Shanghai
200093, China
| | - 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, Vietnam
- Institute of Physics Polish Academy of Sciences
, Al. Lotnikow 32/46, 02-668
Warsaw, Poland
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18
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Bellucci L, Bussi G, Di Felice R, Corni S. Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface. NANOSCALE 2017; 9:2279-2290. [PMID: 28124697 DOI: 10.1039/c6nr06010b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins in the proximity of inorganic surfaces and nanoparticles may undergo profound adjustments that trigger biomedically relevant processes, such as protein fibrillation. The mechanisms that govern protein-surface interactions at the molecular level are still poorly understood. In this work, we investigate the adsorption onto a gold surface, in water, of an amyloid-β (Aβ) peptide, which is the amyloidogenic peptide involved in Alzheimer's disease. The entire adsorption process, from the peptide in bulk water to its conformational relaxation on the surface, is explored by large-scale atomistic molecular dynamics (MD) simulations. We start by providing a description of the conformational ensemble of Aβ in solution by a 22 μs temperature replica exchange MD simulation, which is consistent with previous results. Then, we obtain a statistical description of how the peptide approaches the gold surface by multiple MD simulations, identifying the preferential gold-binding sites and giving a kinetic picture of the association process. Finally, relaxation of the Aβ conformations at the gold/water interface is performed by a 19 μs Hamiltonian-temperature replica exchange MD simulation. We find that the conformational ensemble of Aβ is strongly perturbed by the presence of the surface. In particular, at the gold/water interface the population of the conformers akin to amyloid fibrils is significantly enriched, suggesting that this extended contact geometry may promote fibrillation.
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Affiliation(s)
- Luca Bellucci
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy.
| | - Giovanni Bussi
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Rosa Di Felice
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy. and Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Stefano Corni
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy.
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19
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Huy PDQ, Vuong QV, La Penna G, Faller P, Li MS. Impact of Cu(II) Binding on Structures and Dynamics of Aβ 42 Monomer and Dimer: Molecular Dynamics Study. ACS Chem Neurosci 2016; 7:1348-1363. [PMID: 27454036 DOI: 10.1021/acschemneuro.6b00109] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The classical force field, which is compatible with the Amber force field 99SB, has been obtained for the interaction of Cu(II) with monomer and dimers of amyloid-β peptides using the coordination where Cu(II) is bound to His6, His13 (or His14), and Asp1 with distorted planar geometry. The newly developed force field and molecular dynamics simulation were employed to study the impact of Cu(II) binding on structures and dynamics of Aβ42 monomer and dimers. It was shown that in the presence of Cu(II) the β content of monomer is reduced substantially compared with the wild-type Aβ42 suggesting that, in accord with experiments, metal ions facilitate formation of amorphous aggregates rather than amyloid fibrils with cross-β structures. In addition, one possible mechanism for amorphous assembly is that the Asp23-Lys28 salt bridge, which plays a crucial role in β sheet formation, becomes more flexible upon copper ion binding to the Aβ N-terminus. The simulation of dimers was conducted with the Cu(II)/Aβ stoichiometric ratios of 1:1 and 1:2. For the 1:1 ratio Cu(II) delays the Aβ dimerization process as observed in a number of experiments. The mechanism underlying this phenomenon is associated with slow formation of interchain salt bridges in dimer as well as with decreased hydrophobicity of monomer upon Cu-binding.
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Affiliation(s)
- Pham Dinh Quoc Huy
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute
for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi
Minh City, Vietnam
| | - Quan Van Vuong
- Institute
for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi
Minh City, Vietnam
- Department
of Chemistry, Nagoya University, Nagoya 464-8602, Japan
| | - Giovanni La Penna
- National Research Council of Italy CNR, Institute
for Chemistry of Organometallic Compounds ICCOM, 50019 Florence, Italy
- Italian Institute for Nuclear Physics INFN, Section
of Roma-Tor Vergata, 50019 Florence, Italy
| | - Peter Faller
- Biometals
and Biological Chemistry, Institute of Chemistry, University of Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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20
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Coskuner O. Divalent copper ion bound amyloid-β(40) and amyloid-β(42) alloforms are less preferred than divalent zinc ion bound amyloid-β(40) and amyloid-β(42) alloforms. J Biol Inorg Chem 2016; 21:957-973. [DOI: 10.1007/s00775-016-1392-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/31/2016] [Indexed: 12/25/2022]
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21
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Nguyen HL, Thi Minh Thu T, Truong PM, Lan PD, Man VH, Nguyen PH, Tu LA, Chen YC, Li MS. Aβ41 Aggregates More Like Aβ40 than Like Aβ42: In Silico and in Vitro Study. J Phys Chem B 2016; 120:7371-9. [DOI: 10.1021/acs.jpcb.6b06368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hoang Linh Nguyen
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Department
of Applied Physics, Faculty of Applied Science, Ho Chi Minh City University of Technology - VNU HCM, 268 Ly Thuong Kiet Street, District
10, Ho Chi Minh City, Vietnam
| | - Tran Thi Minh Thu
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Department
of Applied Physics, Faculty of Applied Science, Ho Chi Minh City University of Technology - VNU HCM, 268 Ly Thuong Kiet Street, District
10, Ho Chi Minh City, Vietnam
| | - Phan Minh Truong
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Pham Dang Lan
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Viet Hoang Man
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire
de
Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ly Anh Tu
- Department
of Applied Physics, Faculty of Applied Science, Ho Chi Minh City University of Technology - VNU HCM, 268 Ly Thuong Kiet Street, District
10, Ho Chi Minh City, Vietnam
| | - Yi-Cheng Chen
- Department
of Medicine, MacKay Medical College, New Taipei City 252, Taiwan
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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22
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Conformational transition of Aβ 42 inhibited by a mimetic peptide. A molecular modeling study using QM/MM calculations and QTAIM analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Singh SK, Srivastav S, Yadav AK, Srikrishna S, Perry G. Overview of Alzheimer's Disease and Some Therapeutic Approaches Targeting Aβ by Using Several Synthetic and Herbal Compounds. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2016:7361613. [PMID: 27034741 PMCID: PMC4807045 DOI: 10.1155/2016/7361613] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/05/2015] [Indexed: 01/10/2023]
Abstract
Alzheimer's disease (AD) is a complex age-related neurodegenerative disease. In this review, we carefully detail amyloid-β metabolism and its role in AD. We also consider the various genetic animal models used to evaluate therapeutics. Finally, we consider the role of synthetic and plant-based compounds in therapeutics.
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Affiliation(s)
- Sandeep Kumar Singh
- Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Saurabh Srivastav
- Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Amarish Kumar Yadav
- Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Saripella Srikrishna
- Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi 221 005, India
| | - George Perry
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA
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24
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Tran L, Ha-Duong T. Exploring the Alzheimer amyloid-β peptide conformational ensemble: A review of molecular dynamics approaches. Peptides 2015; 69:86-91. [PMID: 25908410 DOI: 10.1016/j.peptides.2015.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease is one of the most common dementia among elderly worldwide. There is no therapeutic drugs until now to treat effectively this disease. One main reason is due to the poorly understood mechanism of Aβ peptide aggregation, which plays a crucial role in the development of Alzheimer's disease. It remains challenging to experimentally or theoretically characterize the secondary and tertiary structures of the Aβ monomer because of its high flexibility and aggregation propensity, and its conformations that lead to the aggregation are not fully identified. In this review, we highlight various structural ensembles of Aβ peptide revealed and characterized by computational approaches in order to find converging structures of Aβ monomer. Understanding how Aβ peptide forms transiently stable structures prior to aggregation will contribute to the design of new therapeutic molecules against the Alzheimer's disease.
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Affiliation(s)
- Linh Tran
- BioCIS, UMR CNRS 8076, LabEx LERMIT, Faculty of Pharmacy, University Paris Sud, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France
| | - Tâp Ha-Duong
- BioCIS, UMR CNRS 8076, LabEx LERMIT, Faculty of Pharmacy, University Paris Sud, 5 Rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France.
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25
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Truong PM, Viet MH, Nguyen PH, Hu CK, Li MS. Effect of Taiwan Mutation (D7H) on Structures of Amyloid-β Peptides: Replica Exchange Molecular Dynamics Study. J Phys Chem B 2014; 118:8972-81. [DOI: 10.1021/jp503652s] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Phan Minh Truong
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Man Hoang Viet
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Chin-Kun Hu
- Institute
of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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26
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Jónsson SÆ, Mitternacht S, Irbäck A. Mechanical resistance in unstructured proteins. Biophys J 2014; 104:2725-32. [PMID: 23790381 DOI: 10.1016/j.bpj.2013.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022] Open
Abstract
Single-molecule pulling experiments on unstructured proteins linked to neurodegenerative diseases have measured rupture forces comparable to those for stable folded proteins. To investigate the structural mechanisms of this unexpected force resistance, we perform pulling simulations of the amyloid β-peptide (Aβ) and α-synuclein (αS), starting from simulated conformational ensembles for the free monomers. For both proteins, the simulations yield a set of rupture events that agree well with the experimental data. By analyzing the conformations occurring shortly before rupture in each event, we find that the mechanically resistant structures share a common architecture, with similarities to the folds adopted by Aβ and αS in amyloid fibrils. The disease-linked Arctic mutation of Aβ is found to increase the occurrence of highly force-resistant structures. Our study suggests that the high rupture forces observed in Aβ and αS pulling experiments are caused by structures that might have a key role in amyloid formation.
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Affiliation(s)
- Sigurður Ægir Jónsson
- Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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27
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Coskuner O, Wise-Scira O. Arginine and disordered amyloid-β peptide structures: molecular level insights into the toxicity in Alzheimer's disease. ACS Chem Neurosci 2013; 4:1549-58. [PMID: 24041422 DOI: 10.1021/cn4001389] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recent studies present that the single arginine (R) residue in the sequence of Aβ42 adopts abundant β-sheet structure and forms stable salt bridges with various residues. Furthermore, experiments proposed that R stimulates the Aβ assembly and arginine (R) to alanine (A) mutation (R5A) decreases both aggregate formation tendency and the degree of its toxicity. However, the exact roles of R and R5A mutation in the structures of Aβ42 are poorly understood. Extensive molecular dynamics simulations along with thermodynamic calculations present that R5A mutation impacts the structures and free energy landscapes of the aqueous Aβ42 peptide. The β-sheet structure almost disappears in the Ala21-Ala30 region but is more abundant in parts of the central hydrophobic core and C-terminal regions of Aβ42 upon R5A mutation. More abundant α-helix is adopted in parts of the N-terminal and mid-domain regions and less prominent α-helix formation occurs in the central hydrophobic core region of Aβ42 upon R5A mutation. Interestingly, intramolecular interactions between N- and C-terminal or mid-domain regions disappear upon R5A mutation. The structures of Aβ42 are thermodynamically less stable and retain reduced compactness upon R5A mutation. R5A mutant-type structure stability increases with more prominent central hydrophobic core and mid-domain or C-terminal region interactions. Based on our results reported in this work, small organic molecules and antibodies that avoid β-sheet formation in the Ala21-Ala30 region and hinder the intramolecular interactions occurring between the N-terminal and mid-domain or C-terminal regions of Aβ42 may help to reduce Aβ42 toxicity in Alzheimer's disease.
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Affiliation(s)
- Orkid Coskuner
- Department of Chemistry and ‡Neurosciences
Institute, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Olivia Wise-Scira
- Department of Chemistry and ‡Neurosciences
Institute, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
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28
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Smith MD, Cruz L. Changes to the Structure and Dynamics in Mutations of Aβ21–30 Caused by Ions in Solution. J Phys Chem B 2013; 117:14907-15. [DOI: 10.1021/jp408579v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Micholas Dean Smith
- Department
of Physics, Drexel University, 3141 Chestnut Street, Philadelphia 19104, Pennsylvania, United States
| | - Luis Cruz
- Department
of Physics, Drexel University, 3141 Chestnut Street, Philadelphia 19104, Pennsylvania, United States
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29
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Fisher CK, Ullman O, Stultz CM. Comparative studies of disordered proteins with similar sequences: application to Aβ40 and Aβ42. Biophys J 2013; 104:1546-55. [PMID: 23561531 DOI: 10.1016/j.bpj.2013.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 02/03/2013] [Accepted: 02/08/2013] [Indexed: 12/30/2022] Open
Abstract
Quantitative comparisons of intrinsically disordered proteins (IDPs) with similar sequences, such as mutant forms of the same protein, may provide insights into IDP aggregation-a process that plays a role in several neurodegenerative disorders. Here we describe an approach for modeling IDPs with similar sequences that simplifies the comparison of the ensembles by utilizing a single library of structures. The relative population weights of the structures are estimated using a Bayesian formalism, which provides measures of uncertainty in the resulting ensembles. We applied this approach to the comparison of ensembles for Aβ40 and Aβ42. Bayesian hypothesis testing finds that although both Aβ species sample β-rich conformations in solution that may represent prefibrillar intermediates, the probability that Aβ42 samples these prefibrillar states is roughly an order of magnitude larger than the frequency in which Aβ40 samples such structures. Moreover, the structure of the soluble prefibrillar state in our ensembles is similar to the experimentally determined structure of Aβ that has been implicated as an intermediate in the aggregation pathway. Overall, our approach for comparative studies of IDPs with similar sequences provides a platform for future studies on the effect of mutations on the structure and function of disordered proteins.
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Affiliation(s)
- Charles K Fisher
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts, USA
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30
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Chong SH, Ham S. Assessing the influence of solvation models on structural characteristics of intrinsically disordered protein. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Okamoto A, Yano A, Nomura K, Higai S, Kurita N. Stable conformation of full-length amyloid-β (1–42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.05.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Meral D, Urbanc B. Discrete molecular dynamics study of oligomer formation by N-terminally truncated amyloid β-protein. J Mol Biol 2013; 425:2260-75. [PMID: 23500806 PMCID: PMC3665754 DOI: 10.1016/j.jmb.2013.03.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 03/05/2013] [Indexed: 01/09/2023]
Abstract
In Alzheimer's disease (AD), amyloid β-protein (Aβ) self-assembles into toxic oligomers. Of the two predominant Aβ alloforms, Aβ1-40 and Aβ1-42, the latter is particularly strongly linked to AD. N-terminally truncated and pyroglutamated Aβ peptides were recently shown to seed Aβ aggregation and contribute significantly to Aβ-mediated toxicity, yet their folding and assembly were not explored computationally. Discrete molecular dynamics approach previously captured in vitro-derived distinct Aβ1-40 and Aβ1-42 oligomer size distributions and predicted that the more toxic Aβ1-42 oligomers had more flexible and solvent-exposed N-termini than Aβ1-40 oligomers. Here, we examined oligomer formation of Aβ3-40, Aβ3-42, Aβ11-40, and Aβ11-42 by the discrete molecular dynamics approach. The four N-terminally truncated peptides showed increased oligomerization propensity relative to the full-length peptides, consistent with in vitro findings. Conformations formed by Aβ3-40/42 had significantly more flexible and solvent-exposed N-termini than Aβ1-40/42 conformations. In contrast, in Aβ11-40/42 conformations, the N-termini formed more contacts and were less accessible to the solvent. The compactness of the Aβ11-40/42 conformations was in part facilitated by Val12. Two single amino acid substitutions that reduced and abolished hydrophobicity at position 12, respectively, resulted in a proportionally increased structural variability. Our results suggest that Aβ11-40 and Aβ11-42 oligomers might be less toxic than Aβ1-40 and Aβ1-42 oligomers and offer a plausible explanation for the experimentally observed increased toxicity of Aβ3-40 and Aβ3-42 and their pyroglutamated forms.
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Affiliation(s)
- Derya Meral
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
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33
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Xu L, Shan S, Wang X. Single Point Mutation Alters the Microstate Dynamics of Amyloid β-Protein Aβ42 as Revealed by Dihedral Dynamics Analyses. J Phys Chem B 2013; 117:6206-16. [DOI: 10.1021/jp403288b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Liang Xu
- School of Chemistry, Dalian University of Technology, Dalian 116023, China
| | - Shengsheng Shan
- School of Chemistry, Dalian University of Technology, Dalian 116023, China
| | - Xicheng Wang
- Department of Engineering Mechanics,
State Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China
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34
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Chong SH, Yim J, Ham S. Structural heterogeneity in familial Alzheimer's disease mutants of amyloid-beta peptides. MOLECULAR BIOSYSTEMS 2013; 9:997-1003. [DOI: 10.1039/c2mb25457c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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35
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Lin YS, Pande VS. Effects of familial mutations on the monomer structure of Aβ₄₂. Biophys J 2012; 103:L47-9. [PMID: 23260058 DOI: 10.1016/j.bpj.2012.11.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/15/2012] [Accepted: 11/08/2012] [Indexed: 12/25/2022] Open
Abstract
Amyloid beta (Aβ) peptide plays an important role in Alzheimer's disease. A number of mutations in the Aβ sequence lead to familial Alzheimer's disease, congophilic amyloid angiopathy, or hereditary cerebral hemorrhage with amyloid. Using molecular dynamics simulations of ∼200 μs for each system, we characterize and contrast the consequences of four pathogenic mutations (Italian, Dutch, Arctic, and Iowa) for the structural ensemble of the Aβ monomer. The four familial mutations are found to have distinct consequences for the monomer structure.
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36
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Lemkul JA, Bevan DR. The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease. ACS Chem Neurosci 2012; 3:845-56. [PMID: 23173066 DOI: 10.1021/cn300091a] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 08/27/2012] [Indexed: 12/26/2022] Open
Abstract
The pathogenic aggregation of the amyloid β-peptide (Aβ) is considered a hallmark of the progression of Alzheimer's disease, the leading cause of senile dementia in the elderly and one of the principal causes of death in the United States. In the absence of effective therapeutics, the incidence and economic burden associated with the disease are expected to rise dramatically in the coming decades. Targeting Aβ aggregation is an attractive therapeutic approach, though structural insights into the nature of Aβ aggregates from traditional experiments are elusive, making drug design difficult. Theoretical methods have been used for several years to augment experimental work and drive progress forward in Alzheimer's drug design. In this Review, we will describe how two common techniques, molecular docking and molecular dynamics simulations, are being applied in developing small molecules as effective therapeutics against monomeric, oligomeric, and fibrillated forms of Aβ. Recent successes and important limitations will be discussed, and we conclude by providing a perspective on the future of this field by citing recent examples of sophisticated approaches used to better characterize interactions of small molecules with Aβ and other amyloidogenic proteins.
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Affiliation(s)
- Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David R. Bevan
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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Lemkul JA, Bevan DR. Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce “Off-Pathway” Structures. Biochemistry 2012; 51:5990-6009. [DOI: 10.1021/bi300113x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - David R. Bevan
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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38
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Viet MH, Li MS. Amyloid peptide Aβ40 inhibits aggregation of Aβ42: Evidence from molecular dynamics simulations. J Chem Phys 2012; 136:245105. [DOI: 10.1063/1.4730410] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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39
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Lin YS, Bowman GR, Beauchamp KA, Pande VS. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer. Biophys J 2012; 102:315-24. [PMID: 22339868 DOI: 10.1016/j.bpj.2011.12.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/12/2011] [Accepted: 12/01/2011] [Indexed: 12/21/2022] Open
Abstract
The aggregation of amyloid beta (Aβ) peptides plays an important role in the development of Alzheimer's disease. Despite extensive effort, it has been difficult to characterize the secondary and tertiary structure of the Aβ monomer, the starting point for aggregation, due to its hydrophobicity and high aggregation propensity. Here, we employ extensive molecular dynamics simulations with atomistic protein and water models to determine structural ensembles for Aβ(42), Aβ(40), and Aβ(42)-E22K (the Italian mutant) monomers in solution. Sampling of a total of >700 microseconds in all-atom detail with explicit solvent enables us to observe the effects of peptide length and a pathogenic mutation on the disordered Aβ monomer structural ensemble. Aβ(42) and Aβ(40) have crudely similar characteristics but reducing the peptide length from 42 to 40 residues reduces β-hairpin formation near the C-terminus. The pathogenic Italian E22K mutation induces helix formation in the region of residues 20-24. This structural alteration may increase helix-helix interactions between monomers, resulting in altered mechanism and kinetics of Aβ oligomerization.
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Affiliation(s)
- Yu-Shan Lin
- Department of Chemistry, Stanford University, Stanford, California, USA
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40
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Steckmann T, Awan Z, Gerstman BS, Chapagain PP. Kinetics of peptide secondary structure conversion during amyloid β-protein fibrillogenesis. J Theor Biol 2012; 301:95-102. [DOI: 10.1016/j.jtbi.2012.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Barz B, Urbanc B. Dimer formation enhances structural differences between amyloid β-protein (1-40) and (1-42): an explicit-solvent molecular dynamics study. PLoS One 2012; 7:e34345. [PMID: 22509291 PMCID: PMC3324527 DOI: 10.1371/journal.pone.0034345] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2011] [Accepted: 02/26/2012] [Indexed: 11/18/2022] Open
Abstract
Amyloid β-protein (Aβ) is central to the pathology of Alzheimer's disease. A 5% difference in the primary structure of the two predominant alloforms, Aβ(1-40) and Aβ(1-42), results in distinct assembly pathways and toxicity properties. Discrete molecular dynamics (DMD) studies of Aβ(1-40) and Aβ(1-42) assembly resulted in alloform-specific oligomer size distributions consistent with experimental findings. Here, a large ensemble of DMD-derived Aβ(1-40) and Aβ(1-42) monomers and dimers was subjected to fully atomistic molecular dynamics (MD) simulations using the OPLS-AA force field combined with two water models, SPCE and TIP3P. The resulting all-atom conformations were slightly larger, less compact, had similar turn and lower β-strand propensities than those predicted by DMD. Fully atomistic Aβ(1-40) and Aβ(1-42) monomers populated qualitatively similar free energy landscapes. In contrast, the free energy landscape of Aβ(1-42) dimers indicated a larger conformational variability in comparison to that of Aβ(1-40) dimers. Aβ(1-42) dimers were characterized by an increased flexibility in the N-terminal region D1-R5 and a larger solvent exposure of charged amino acids relative to Aβ(1-40) dimers. Of the three positively charged amino acids, R5 was the most and K16 the least involved in salt bridge formation. This result was independent of the water model, alloform, and assembly state. Overall, salt bridge propensities increased upon dimer formation. An exception was the salt bridge propensity of K28, which decreased upon formation of Aβ(1-42) dimers and was significantly lower than in Aβ(1-40) dimers. The potential relevance of the three positively charged amino acids in mediating the Aβ oligomer toxicity is discussed in the light of available experimental data.
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Affiliation(s)
- Bogdan Barz
- Physics Department, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Brigita Urbanc
- Physics Department, Drexel University, Philadelphia, Pennsylvania, United States of America
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42
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Wise-Scira O, Xu L, Kitahara T, Perry G, Coskuner O. Amyloid-β peptide structure in aqueous solution varies with fragment size. J Chem Phys 2012; 135:205101. [PMID: 22128957 DOI: 10.1063/1.3662490] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Various fragment sizes of the amyloid-β (Aβ) peptide have been utilized to mimic the properties of the full-length Aβ peptide in solution. Among these smaller fragments, Aβ16 and Aβ28 have been investigated extensively. In this work, we report the structural and thermodynamic properties of the Aβ16, Aβ28, and Aβ42 peptides in an aqueous solution environment. We performed replica exchange molecular dynamics simulations along with thermodynamic calculations for investigating the conformational free energies, secondary and tertiary structures of the Aβ16, Aβ28, and Aβ42 peptides. The results show that the thermodynamic properties vary from each other for these peptides. Furthermore, the secondary structures in the Asp1-Lys16 and Asp1-Lys28 regions of Aβ42 cannot be completely captured by the Aβ16 and Aβ28 fragments. For example, the β-sheet structures in the N-terminal region of Aβ16 and Aβ28 are either not present or the abundance is significantly decreased in Aβ42. The α-helix and β-sheet abundances in Aβ28 and Aβ42 show trends--to some extent--with the potential of mean forces but no such trend could be obtained for Aβ16. Interestingly, Arg5 forms salt bridges with large abundances in all three peptides. The formation of a salt bridge between Asp23-Lys28 is more preferred over the Glu22-Lys28 salt bridge in Aβ28 but this trend is vice versa for Aβ42. This study shows that the Asp1-Lys16 and Asp1-Lys28 regions of the full length Aβ42 peptide cannot be completely mimicked by studying the Aβ16 and Aβ28 peptides.
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Affiliation(s)
- Olivia Wise-Scira
- The University of Texas at San Antonio, Department of Chemistry, One UTSA Circle, San Antonio, Texas 78249, USA
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Chong SH, Park M, Ham S. Structural and Thermodynamic Characteristics That Seed Aggregation of Amyloid-β Protein in Water. J Chem Theory Comput 2012; 8:724-34. [DOI: 10.1021/ct200757a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Song-Ho Chong
- Department
of Chemistry, Sookmyung Women’s University,
Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
| | - Mirae Park
- Department
of Chemistry, Sookmyung Women’s University,
Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
| | - Sihyun Ham
- Department
of Chemistry, Sookmyung Women’s University,
Hyochangwon-gil 52, Yongsan-gu, Seoul, 140-742, Korea
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