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Heid LF, Agerschou ED, Orr AA, Kupreichyk T, Schneider W, Wördehoff MM, Schwarten M, Willbold D, Tamamis P, Stoldt M, Hoyer W. Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation. Comput Struct Biotechnol J 2024; 23:417-430. [PMID: 38223341 PMCID: PMC10787225 DOI: 10.1016/j.csbj.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
β-Structure-rich amyloid fibrils are hallmarks of several diseases, including Alzheimer's (AD), Parkinson's (PD), and type 2 diabetes (T2D). While amyloid fibrils typically consist of parallel β-sheets, the anti-parallel β-hairpin is a structural motif accessible to amyloidogenic proteins in their monomeric and oligomeric states. Here, to investigate implications of β-hairpins in amyloid formation, potential β-hairpin-forming amyloidogenic segments in the human proteome were predicted based on sequence similarity with β-hairpins previously observed in Aβ, α-synuclein, and islet amyloid polypeptide, amyloidogenic proteins associated with AD, PD, and T2D, respectively. These three β-hairpins, established upon binding to the engineered binding protein β-wrapin AS10, are characterized by proximity of two sequence segments rich in hydrophobic and aromatic amino acids, with high β-aggregation scores according to the TANGO algorithm. Using these criteria, 2505 potential β-hairpin-forming amyloidogenic segments in 2098 human proteins were identified. Characterization of a test set of eight protein segments showed that seven assembled into Thioflavin T-positive aggregates and four formed β-hairpins in complex with AS10 according to NMR. One of those is a segment of prostatic acid phosphatase (PAP) comprising amino acids 185-208. PAP is naturally cleaved into fragments, including PAP(248-286) which forms functional amyloid in semen. We find that PAP(185-208) strongly decreases the protein concentrations required for fibril formation of PAP(248-286) and of another semen amyloid peptide, SEM1(86-107), indicating that it promotes nucleation of semen amyloids. In conclusion, β-hairpin-forming amyloidogenic protein segments could be identified in the human proteome with potential roles in functional or disease-related amyloid formation.
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Affiliation(s)
- Laetitia F. Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Emil Dandanell Agerschou
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, United States
| | - Tatsiana Kupreichyk
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Walfried Schneider
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Michael M. Wördehoff
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Melanie Schwarten
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3033, United States
| | - Matthias Stoldt
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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2
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Heid LF, Kupreichyk T, Schützmann MP, Schneider W, Stoldt M, Hoyer W. Nucleation of α-Synuclein Amyloid Fibrils Induced by Cross-Interaction with β-Hairpin Peptides Derived from Immunoglobulin Light Chains. Int J Mol Sci 2023; 24:16132. [PMID: 38003322 PMCID: PMC10671648 DOI: 10.3390/ijms242216132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Heterologous interactions between different amyloid-forming proteins, also called cross-interactions, may have a critical impact on disease-related amyloid formation. β-hairpin conformers of amyloid-forming proteins have been shown to affect homologous interactions in the amyloid self-assembly process. Here, we applied two β-hairpin-forming peptides derived from immunoglobulin light chains as models to test how heterologous β-hairpins modulate the fibril formation of Parkinson's disease-associated protein α-synuclein (αSyn). The peptides SMAhp and LENhp comprise β-strands C and C' of the κ4 antibodies SMA and LEN, which are associated with light chain amyloidosis and multiple myeloma, respectively. SMAhp and LENhp bind with high affinity to the β-hairpin-binding protein β-wrapin AS10 according to isothermal titration calorimetry and NMR spectroscopy. The addition of SMAhp and LENhp affects the kinetics of αSyn aggregation monitored by Thioflavin T (ThT) fluorescence, with the effect depending on assay conditions, salt concentration, and the applied β-hairpin peptide. In the absence of agitation, substoichiometric concentrations of the hairpin peptides strongly reduce the lag time of αSyn aggregation, suggesting that they support the nucleation of αSyn amyloid fibrils. The effect is also observed for the aggregation of αSyn fragments lacking the N-terminus or the C-terminus, indicating that the promotion of nucleation involves the interaction of hairpin peptides with the hydrophobic non-amyloid-β component (NAC) region.
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Affiliation(s)
- Laetitia F. Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Tatsiana Kupreichyk
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marie P. Schützmann
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Walfried Schneider
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Matthias Stoldt
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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3
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Co NT, Lan PD, Quoc Huy PD, Li MS. Heat-induced degradation of fibrils: Exponential vs logistic kinetics. J Chem Phys 2020; 152:115101. [PMID: 32199422 DOI: 10.1063/1.5144305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The degradation of fibrils under the influence of thermal fluctuations was studied experimentally by various groups around the world. In the first set of experiments, it was shown that the decay of fibril content, which can be measured by the ThT fluorescence assay, obeys a bi-exponential function. In the second series of experiments, it was demonstrated that when the monomers separated from the aggregate are not recyclable, the time dependence of the number of monomers belonging to the dominant cluster is described by a single-exponential function if the fraction of bound chains becomes less than a certain threshold. Note that the time dependence of the fraction of bound chains can be measured by tryptophan fluorescence. To understand these interesting experimental results, we developed a phenomenological theory and performed molecular simulation. According to our theory and simulations using the lattice and all-atom models, the time dependence of bound chains is described by a logistic function, which slowly decreases at short time scales but becomes a single exponential function at large time scales. The results, obtained by using lattice and all-atom simulations, ascertained that the time dependence of the fibril content can be described by a bi-exponential function that decays faster than the logistic function on short time scales. We have uncovered the molecular mechanism for the distinction between the logistic and bi-exponential behavior. Since the dissociation of the chain from the fibrils requires the breaking of a greater number of inter-chain contacts as compared to the breaking of the beta sheet structure, the decrease in the number of connected chains is slower than the fibril content. Therefore, the time dependence of the aggregate size is logistic, while the two-exponential behavior is preserved for the content of fibrils. Our results are in agreement with the results obtained in both sets of experiments.
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Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - 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
| | - Pham Dinh Quoc Huy
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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4
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Press-Sandler O, Miller Y. Distinct Primary Nucleation of Polymorphic Aβ Dimers Yields to Distinguished Fibrillation Pathways. ACS Chem Neurosci 2019; 10:4407-4413. [PMID: 31532176 DOI: 10.1021/acschemneuro.9b00437] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Polymorphic Aβ dimers are the smallest toxic species that play a role in the pathology of Alzheimer's disease. There is great interest in understanding the malfunctions that yield to these toxic species and in providing insights into the molecular mechanisms of the primary nucleation. Herein, we present a first work that demonstrates two distant edges states of Aβ dimers. The first is the so-called "random coil" state dimer that mimics the primary seeding/nucleation that is far from a fibrillation state. The second is the "fibril-like" state dimer that is structurally in close proximity to the fibril, a well-organized state into a fibril-like structure. We show for the first time that a conformational change of one monomer within the dimer impedes primary nucleation, while less fluctuations and relatively large number of interactions in nucleation domains induce the primary nucleation to produce toxic stable species. Overall, the current study exhibits a diversity of primary nucleation in each dimer state, suggesting distinct molecular mechanisms of fibril formation. The conformations of the early stage Aβ dimers that were achieved may provide crucial data for designing inhibitors to impede the primary nucleation.
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Affiliation(s)
- Olga Press-Sandler
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
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5
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Liang C, Savinov SN, Fejzo J, Eyles SJ, Chen J. Modulation of Amyloid-β42 Conformation by Small Molecules Through Nonspecific Binding. J Chem Theory Comput 2019; 15:5169-5174. [PMID: 31476124 PMCID: PMC6783347 DOI: 10.1021/acs.jctc.9b00599] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Aggregation of amyloid-β (Aβ) peptides is a crucial step in the progression of Alzheimer's disease (AD). Identifying aggregation inhibitors against AD has been a great challenge. We report an atomistic simulation study of the inhibition mechanism of two small molecules, homotaurine and scyllo-inositol, which are AD drug candidates currently under investigation. We show that both small molecules promote a conformational change of the Aβ42 monomer toward a more collapsed phase through a nonspecific binding mechanism. This finding provides atomistic-level insights into designing potential drug candidates for future AD treatments.
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Affiliation(s)
- Chungwen Liang
- Computational Modeling Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Sergey N Savinov
- Computational Modeling Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
- Department of Biochemistry and Molecular Biology , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Jasna Fejzo
- Biomolecular NMR Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS) , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biology , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
- Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
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6
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Churchill CDM, Healey MA, Preto J, Tuszynski JA, Woodside MT. Probing the Basis of α-Synuclein Aggregation by Comparing Simulations to Single-Molecule Experiments. Biophys J 2019; 117:1125-1135. [PMID: 31477241 DOI: 10.1016/j.bpj.2019.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/21/2019] [Accepted: 08/12/2019] [Indexed: 11/29/2022] Open
Abstract
Intrinsically disordered proteins often play an important role in protein aggregation. However, it is challenging to determine the structures and interactions that drive the early stages of aggregation because they are transient and obscured in a heterogeneous mixture of disordered states. Even computational methods are limited because the lack of ordered structure makes it difficult to ensure that the relevant conformations are sampled. We address these challenges by integrating atomistic simulations with high-resolution single-molecule measurements reported previously, using the measurements to help discern which parts of the disordered ensemble of structures in the simulations are most probable while using the simulations to identify residues and interactions that are important for oligomer stability. This approach was applied to α-synuclein, an intrinsically disordered protein that aggregates in the context of Parkinson's disease. We simulated single-molecule pulling experiments on dimers, the minimal oligomer, and compared them to force spectroscopy measurements. Force-extension curves were simulated starting from a set of 66 structures with substantial structured content selected from the ensemble of dimer structures generated at zero force via Monte Carlo simulations. The pattern of contour length changes as the structures unfolded through intermediate states was compared to the results from optical trapping measurements on the same dimer to discern likely structures occurring in the measurements. Simulated pulling curves were generally consistent with experimental data but with a larger number of transient intermediates. We identified an ensemble of β-rich dimer structures consistent with the experimental data from which dimer interfaces could be deduced. These results suggest specific druggable targets in the structural motifs of α-synuclein that may help prevent the earliest steps of oligomerization.
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Affiliation(s)
| | - Mark A Healey
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Jordane Preto
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada; Department of Oncology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada.
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7
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Hilt S, Rojalin T, Viitala T, Koivuniemi A, Bunker A, Hogiu SW, Kálai T, Hideg K, Yliperttula M, Voss JC. Oligomerization Alters Binding Affinity Between Amyloid Beta and a Modulator of Peptide Aggregation. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2017; 121:23974-23987. [PMID: 30214656 PMCID: PMC6130836 DOI: 10.1021/acs.jpcc.7b06164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The soluble oligomeric form of the amyloid beta (Aβ) peptide is the major causative agent in the molecular pathogenesis of Alzheimer's disease (AD). We have previously developed a pyrroline-nitroxyl fluorene compound (SLF) that blocks the toxicity of Aβ. Here we introduce the multi-parametric surface plasmon resonance (MP-SPR) approach to quantify SLF binding and effect on the self-association of the peptide via a label-free, real-time approach. Kinetic analysis of SLF binding to Aβ and measurements of layer thickness alterations inform on the mechanism underlying the ability of SLF to inhibit Aβ toxicity and its progression towards larger oligomeric assemblies. Depending on the oligomeric state of Aβ, distinct binding affinities for SLF are revealed. The Aβ monomer and dimer uniquely possess sub-nanomolar affinity for SLF via a non-specific mode of binding. SLF binding is weaker in oligomeric Aβ, which displays an affinity for SLF on the order of 100 μM. To complement these experiments we carried out molecular docking and molecular dynamics simulations to explore how SLF interacts with the Aβ peptide. The MP-SPR results together with in silico modeling provide affinity data for the SLF-Aβ interaction and allow us to develop a new general method for examining protein aggregation.
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Affiliation(s)
- Silvia Hilt
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Tatu Rojalin
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Tapani Viitala
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Artturi Koivuniemi
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Alex Bunker
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
| | - Sebastian Wachsmann Hogiu
- Department of Pathology and Laboratory Medicine, and Center for Biophotonics, University of California Davis, USA
- Intellectual Ventures/Global Good, Bellevue, WA, USA
| | - Tamás Kálai
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Kálmán Hideg
- Institute of Organic and Medicinal Chemistry, University of Pécs, H 7624 Pécs, Szigeti st. 12. Pécs, Hungary
| | - Marjo Yliperttula
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Finland
- Department of Pharmaceutical Sciences, University of Padova, Italy
| | - John C. Voss
- Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
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8
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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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9
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Study of structural stability and damaging effect on membrane for four Aβ42 dimers. PLoS One 2017; 12:e0179147. [PMID: 28594887 PMCID: PMC5464659 DOI: 10.1371/journal.pone.0179147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/24/2017] [Indexed: 11/19/2022] Open
Abstract
Increasing evidence shows that Aβ oligomers are key pathogenic molecules in Alzheimer’s disease. Among Aβ oligomers, dimer is the smallest aggregate and toxic unit. Therefore, understanding its structural and dynamic properties is quite useful to prevent the formation and toxicity of the Aβ oligomers. In this study, we performed molecular dynamic simulations on four Aβ42 dimers, 2NCb, CNNC, NCNC and NCCN, within the hydrated DPPC membrane. Four Aβ42 dimers differ in the arrangements of two Aβ42 peptides. This study aims to investigate the impact of aggregation pattern of two Aβ peptides on the structural stability of the Aβ42 dimer and its disruption to the biological membrane. The MD results demonstrate that the NCCN, CNNC and NCNC have the larger structural fluctuation at the N-terminus of Aβ42 peptide, where the β-strand structure converts into the coil structure. The loss of the N-terminal β-strand further impairs the aggregate ability of Aβ42 dimer. In addition, inserting Aβ42 dimer into the membrane can considerably decrease the average APL of DPPC membrane. Moreover this decrease effect is largely dependent on the distance to the location of Aβ42 dimer and its secondary structure forms. Based on the results, the 2NCb is considered as a stable dimeric unit for aggregating the larger Aβ42 oligomer, and has a potent ability to disrupt the membrane.
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10
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Man VH, Nguyen PH, Derreumaux P. Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers. J Phys Chem B 2017; 121:2434-2442. [PMID: 28245647 PMCID: PMC5944329 DOI: 10.1021/acs.jpcb.7b00267] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We characterized the dimer of the amyloid-β wild-type (WT) peptide, Aβ, of 42 residues and its disulfide-bond-locked double mutant (S8C) by replica exchange molecular dynamics simulations. Aβ dimers are known to be the smallest toxic species in Alzheimer's disease, and the S8C mutant has been shown experimentally to form an exclusive homogeneous and neurotoxic dimer. Our 50 μs all-atom simulations reveal similar secondary structures and collision cross-sections but very different intramolecular and intermolecular conformations upon double S8C mutation. Both dimers are very dynamic with hundreds of free-energy minima that differ from the U-shape and S-shape conformations of the peptides in the fibrils. The only common structural feature, shared by both species with a probability of 4% in WT and 12% in S8C-S8C, is a three-stranded β-sheet spanning the 17-23, 29-36, and 39-41 residues, which does not exist in the Aβ40 WT dimers.
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Affiliation(s)
- Viet Hoang Man
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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11
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Das P, Chacko AR, Belfort G. Alzheimer's Protective Cross-Interaction between Wild-Type and A2T Variants Alters Aβ 42 Dimer Structure. ACS Chem Neurosci 2017; 8:606-618. [PMID: 28292185 DOI: 10.1021/acschemneuro.6b00357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing has recently revealed the protective effect of a single A2T mutation in heterozygous carriers against Alzheimer's disease (AD) and age-related cognitive decline. The impact of the protective cross-interaction between the wild-type (WT) and A2T variants on the dimer structure is therefore of high interest, as the Aβ dimers are the smallest known neurotoxic species. Toward this goal, extensive atomistic replica exchange molecular dynamics simulations of the solvated WT homo- and A2T hetero- Aβ1-42 dimers have been performed, resulting into a total of 51 μs of sampling for each system. Weakening of a set of transient, intrachain contacts formed between the central and C-terminal hydrophobic residues is observed in the heterodimeric system. The majority of the heterodimers with reduced interaction between central and C-terminal regions lack any significant secondary structure and display a weak interchain interface. Interestingly, the A2T N-terminus, particularly residue F4, is frequently engaged in tertiary and quaternary interactions with central and C-terminal hydrophobic residues in those distinct structures, leading to hydrophobic burial. This atypical involvement of the N-terminus within A2T heterodimer revealed in our simulations implies possible interference on Aβ42 aggregation and toxic oligomer formation, which is consistent with experiments. In conclusion, the present study provides detailed structural insights onto A2T Aβ42 heterodimer, which might provide molecular insights onto the AD protective effect of the A2T mutation in the heterozygous state.
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Affiliation(s)
- Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Anita R. Chacko
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Georges Belfort
- Howard
P. Isermann Department of Chemical and Biological Engineering, and
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180-3590, United States
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12
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Zhang Y, Hashemi M, Lv Z, Lyubchenko YL. Self-assembly of the full-length amyloid Aβ42 protein in dimers. NANOSCALE 2016; 8:18928-18937. [PMID: 27714140 PMCID: PMC5114164 DOI: 10.1039/c6nr06850b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The self-assembly of amyloid (Aβ) proteins into nano-aggregates is a hallmark of Alzheimer's disease (AD) development, yet the mechanism of how disordered monomers assemble into aggregates remains elusive. Here, we applied long-time molecular dynamics simulations to fully characterize the assembly of Aβ42 monomers into dimers. Monomers undergo conformational changes during their interaction, but the resulting dimer structures do not resemble those found in fibril structures. To identify natural conformations of dimers among a set of simulated ones, validation approaches were developed and applied, and a subset of dimer conformations were characterized. These dimers do not contain long β-strands that are usually found in fibrils. The dimers are stabilized primarily by interactions within the central hydrophobic regions and the C-terminal regions, with a contribution from local hydrogen bonding. The dimers are dynamic, as evidenced by the existence of a set of conformations and by the quantitative analyses of the dimer dissociation process.
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Affiliation(s)
- Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 69198, USA.
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13
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Bille A, Mohanty S, Irbäck A. Peptide folding in the presence of interacting protein crowders. J Chem Phys 2016; 144:175105. [PMID: 27155657 DOI: 10.1063/1.4948462] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.
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Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Sandipan Mohanty
- Jülich Supercomputing Centre, Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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14
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Zheng Y, Tian S, Peng X, Yang J, Fu Y, Jiao Y, Zhao J, He J, Hong T. Kinesin-1 inhibits the aggregation of amyloid-β peptide as detected by fluorescence cross-correlation spectroscopy. FEBS Lett 2016; 590:1028-37. [DOI: 10.1002/1873-3468.12137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 02/04/2016] [Accepted: 03/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Yanpeng Zheng
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Shijun Tian
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Xianglei Peng
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Jingfa Yang
- Beijing National Laboratory for Molecular Science; Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Yuanhui Fu
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Yueying Jiao
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Jiang Zhao
- Beijing National Laboratory for Molecular Science; Institute of Chemistry; Chinese Academy of Sciences; Beijing China
| | - Jinsheng He
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
| | - Tao Hong
- College of Life Sciences and Bioengineering; Beijing Jiaotong University; China
- Institute for Viral Disease Control and Prevention; Chinese Centre for Disease Control and Prevention; Beijing China
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15
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Tran L, Basdevant N, Prévost C, Ha-Duong T. Structure of ring-shaped Aβ₄₂ oligomers determined by conformational selection. Sci Rep 2016; 6:21429. [PMID: 26868929 PMCID: PMC4751476 DOI: 10.1038/srep21429] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/22/2016] [Indexed: 11/28/2022] Open
Abstract
The oligomerization of amyloid beta (Aβ) peptides into soluble non-fibrillar species plays a critical role in the pathogenesis of Alzheimer’s disease. However, it has been challenging to characterize the tertiary and quaternary structures of Aβ peptides due to their disordered nature and high aggregation propensity. In this work, replica exchange molecular dynamics simulations were used to explore the conformational space of Aβ42 monomer. Among the most populated transient states, we identified a particular conformation which was able to generate ring-shaped pentamers and hexamers, when docked onto itself. The structures of these aggregates were stable during microsecond all-atom MD simulations in explicit solvent. In addition to high resolution models of these oligomers, this study provides support for the conformational selection mechanism of Aβ peptide self-assembly.
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Affiliation(s)
- Linh Tran
- BIOCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, 92290, France
| | | | - Chantal Prévost
- LBT, Univ. Paris-Diderot, CNRS, Sorbonne Paris-Cité, Paris, 75005 France
| | - Tâp Ha-Duong
- BIOCIS, Univ. Paris-Sud, CNRS, Université Paris-Saclay, Châtenay-Malabry, 92290, France
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16
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Tian P, Lindorff-Larsen K, Boomsma W, Jensen MH, Otzen DE. A Monte Carlo Study of the Early Steps of Functional Amyloid Formation. PLoS One 2016; 11:e0146096. [PMID: 26745180 PMCID: PMC4706413 DOI: 10.1371/journal.pone.0146096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/14/2015] [Indexed: 11/18/2022] Open
Abstract
In addition to their well-known roles in neurodegenerative diseases and amyloidoses, amyloid structures also assume important functional roles in the cell. Although functional amyloid shares many physiochemical properties with its pathogenic counterpart, it is evolutionarily optimized to avoid cytotoxicity. This makes it an interesting study case for aggregation phenomenon in general. One of the most well-known examples of a functional amyloid, E. coli curli, is an essential component in the formation of bacterial biofilm, and is primarily formed by aggregates of the protein CsgA. Previous studies have shown that the minor sequence variations observed in the five different subrepeats (R1-R5), which comprise the CsgA primary sequence, have a substantial influence on their individual aggregation propensities. Using a recently described diffusion-optimized enhanced sampling approach for Monte Carlo simulations, we here investigate the equilibrium properties of the monomeric and dimeric states of these subrepeats, to probe whether structural properties observed in these early stage oligomers are decisive for the characteristics of the resulting aggregate. We show that the dimerization propensities of these peptides have strong correlations with their propensity for amyloid formation, and provide structural insights into the inter- and intramolecular contacts that appear to be essential in this process.
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Affiliation(s)
- Pengfei Tian
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.,Linderstrøm-Lang Centre for Protein Science and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Linderstrøm-Lang Centre for Protein Science and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Mogens Høgh Jensen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, 8000, Aarhus C, Denmark
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17
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Bille A, Linse B, Mohanty S, Irbäck A. Equilibrium simulation of trp-cage in the presence of protein crowders. J Chem Phys 2015; 143:175102. [DOI: 10.1063/1.4934997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Björn Linse
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Sandipan Mohanty
- Institute for Advanced Simulation, Jülich Supercomputing Centre, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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18
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 478] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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19
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Shaykhalishahi H, Mirecka EA, Gauhar A, Grüning CSR, Willbold D, Härd T, Stoldt M, Hoyer W. A β-Hairpin-Binding Protein for Three Different Disease-Related Amyloidogenic Proteins. Chembiochem 2014; 16:411-4. [DOI: 10.1002/cbic.201402552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Indexed: 12/12/2022]
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20
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Pouplana R, Campanera JM. Energetic contributions of residues to the formation of early amyloid-β oligomers. Phys Chem Chem Phys 2014; 17:2823-37. [PMID: 25503571 DOI: 10.1039/c4cp04544k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-weight amyloid-β (Aβ) oligomers formed at early stages of oligomerization rather than fibril assemblies seem to be the toxic components that drive neurodegeneration in Alzheimer's disease. Unfortunately, detailed knowledge of the structure of these early oligomers at the residue level is not yet available. In this study, we performed all-atom explicit solvent molecular dynamics simulations to examine the oligomerization process of Aβ10-35 monomers when forming dimers, trimers, tetramers and octamers, with four independent simulations of a total simulated time of 3 μs for each oligomer system. The decomposition of the stability free energy by MM-GBSA methodology allowed us to unravel the network of energetic interactions that stabilize such oligomers. The contribution of the intermonomeric van der Waals term is the most significant energy feature of the oligomerization process, consistent with the so-called hydrophobic effect. Furthermore, the decomposition of the stability free energy into residues and residue-pairwise terms revealed that it is mainly apolar interactions between the three specific hydrophobic fragments 31-35 (C-terminal region), 17-20 (central hydrophobic core) and 12-14 (N-terminal region) that are responsible for such a favourable effect. The conformation in which the hydrophobic cthr-chc interaction is oriented perpendicularly is particularly important. We propose three other model substructures that favour the oligomerization process and can thus be considered as molecular targets for future inhibitors. Understanding Aβ oligomerization at the residue level could lead to more efficient design of inhibitors of this process.
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Affiliation(s)
- R Pouplana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII, s/n, Diagonal Sud, 08028, Barcelona, Catalonia, Spain.
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21
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Tsigelny IF, Sharikov Y, Kouznetsova VL, Greenberg JP, Wrasidlo W, Gonzalez T, Desplats P, Michael SE, Trejo-Morales M, Overk CR, Masliah E. Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation. J Alzheimers Dis 2014; 39:583-600. [PMID: 24240640 DOI: 10.3233/jad-131589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer's disease (AD) is associated with the formation of toxic amyloid-β (Aβ)42 oligomers, and recent evidence supports a role for Aβ dimers as building blocks for oligomers. Molecular dynamics simulation studies have identified clans for the dominant conformations of Aβ42 forming dimers; however, it is unclear if a larger spectrum of dimers is involved and which set(s) of dimers might evolve to oligomers verse fibrils. Therefore, for this study we generated multiple structural conformations of Aβ42, using explicit all-atom molecular dynamics, and then clustering the different structures based on key conformational similarities. Those matching a selection threshold were then used to model a process of oligomerization. Remarkably, we showed a greater diversity in Aβ dimers than previously described. Depending on the clan family, different types of Aβ dimers were obtained. While some had the tendency to evolve into oligomeric rings, others formed fibrils of diverse characteristics. Then we selected the dimers that would evolve to membranephilic annular oligomers. Nearly one third of the 28 evaluated annular oligomers had the dimer interfaces between the neighboring Aβ42 monomers with possible salt bridges between the residue K28 from one side and either residue E22 or D23 on the other. Based on these results, key amino acids were identified for point mutations that either enhanced or suppressed the formation and toxicity of oligomer rings. Our studies suggest a greater diversity of Aβ dimers. Understanding the structure of Aβ dimers might be important for the rationale design of small molecules that block formation of toxic oligomers.
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Affiliation(s)
- Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Yuriy Sharikov
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jerry P Greenberg
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Wolfgang Wrasidlo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Tania Gonzalez
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Paula Desplats
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Sarah E Michael
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Cassia R Overk
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA Department of Pathology, University of California, San Diego, La Jolla, CA, USA
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22
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Petrlova J, Bhattacherjee A, Boomsma W, Wallin S, Lagerstedt JO, Irbäck A. Conformational and aggregation properties of the 1-93 fragment of apolipoprotein A-I. Protein Sci 2014; 23:1559-71. [PMID: 25131953 DOI: 10.1002/pro.2534] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/11/2014] [Accepted: 08/04/2014] [Indexed: 11/12/2022]
Abstract
Several disease-linked mutations of apolipoprotein A-I, the major protein in high-density lipoprotein (HDL), are known to be amyloidogenic, and the fibrils often contain N-terminal fragments of the protein. Here, we present a combined computational and experimental study of the fibril-associated disordered 1-93 fragment of this protein, in wild-type and mutated (G26R, S36A, K40L, W50R) forms. In atomic-level Monte Carlo simulations of the free monomer, validated by circular dichroism spectroscopy, we observe changes in the position-dependent β-strand probability induced by mutations. We find that these conformational shifts match well with the effects of these mutations in thioflavin T fluorescence and transmission electron microscopy experiments. Together, our results point to molecular mechanisms that may have a key role in disease-linked aggregation of apolipoprotein A-I.
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Affiliation(s)
- Jitka Petrlova
- Department of Experimental Medical Science, Lund University, BMC Floor C12, SE-221 84, Lund, Sweden
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23
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Viet MH, Nguyen PH, Derreumaux P, Li MS. Effect of the English familial disease mutation (H6R) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci 2014; 5:646-57. [PMID: 24949887 DOI: 10.1021/cn500007j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The self-assembly of the amyloid beta (Aβ) peptides into senile plaques is the hallmark of Alzheimer's disease. Recent experiments have shown that the English familial disease mutation (H6R) speeds up the fibril formation process of alloforms Aβ40 and Aβ42 peptides altering their toxicity to cells. We used all-atom molecular dynamics simulations at microsecond time scales with the OPLS-AA force field and TIP4P explicit water model to study the structural dynamics of the monomer and dimer of H6R sequences of both peptides. The reason behind the self-assembly acceleration is common that upon mutation the net charge is reduced leading to the weaker repulsive interaction between chains that facilitates the peptide association. In addition, our estimation of the solvation free energy shows that the mutation enhances the hydrophobicity of both peptides speeding up their aggregation. However, we can show that the acceleration mechanisms are different for different peptides: the rate of fibril formation of Aβ42 increases due to increased β-structure at the C-terminal in both monomer and dimer and enhanced stability of salt bridge Asp23-Lys28 in monomer, while the enhancement of turn at residues 25-29 and reduction of coil in regions 10-13, 26-19, and 30-34 would play the key role for Aβ40. Overall, our study provides a detailed atomistic picture of the H6R-mediated conformational changes that are consistent with the experimental findings and highlights the important role of the N-terminal in Aβ peptide aggregation.
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Affiliation(s)
- 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
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Denis Diderot, Paris Sorbonne Cité 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, Bvd Saint Michel, 75005 Paris, France
| | - Mai Suan Li
- 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
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24
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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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25
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Zhang T, Xu W, Mu Y, Derreumaux P. Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity. ACS Chem Neurosci 2014; 5:148-59. [PMID: 24246047 DOI: 10.1021/cn400197x] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aggregation of the amyloid β protein (Aβ) peptide with 40 or 42 residues is one key feature in Alzheimer's disease (AD). The 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp) molecule was reported to alter Aβ self-assembly and reduce toxicity. Though nuclear magnetic resonance experiments and various simulations provided atomic information about the interaction of NQTrp with Aβ peptides spanning the regions of residues 12-28 and 17-42, none of these studies were conducted on the full-length Aβ1-42 peptide. To this end, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer with two NQTrp molecules in explicit solvent, by using a force field known to fold diverse proteins correctly. The interactions between NQTrp and Aβ1-42, which change the Aβ interface by reducing most of the intermolecular contacts, are found to be very dynamic and multiple, leading to many transient binding sites. The most favorable binding residues are Arg5, Asp7, Tyr10, His13, Lys16, Lys18, Phe19/Phe20, and Leu34/Met35, providing therefore a completely different picture from in vitro and in silico experiments with NQTrp with shorter Aβ fragments. Importantly, the 10 hot residues that we identified explain the beneficial effect of NQTrp in reducing both the level of Aβ1-42 aggregation and toxicity. Our results also indicate that there is room to design more efficient drugs targeting Aβ1-42 dimer against AD.
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Affiliation(s)
- Tong Zhang
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- State Key Laboratory of Precision Spectroscopy, Department
of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université
Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France
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26
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Gill AC. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides. PLoS One 2014; 9:e87354. [PMID: 24498083 PMCID: PMC3909104 DOI: 10.1371/journal.pone.0087354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023] Open
Abstract
Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109-122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109-122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109-122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106-126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new atomic-level model for the formation of oligomers and fibrils of the prion protein and suggest that stabilization of β-hairpin structure may enhance cellular toxicity by altering the balance between oligomeric and fibrillar protein assemblies.
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Affiliation(s)
- Andrew C. Gill
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus, University of Edinburgh, Roslin, Edinburgh, United Kingdom
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27
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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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28
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Smith MD, Srinivasa Rao J, Cruz L. Spontaneous dimer states of the Aβ21–30decapeptide. Phys Chem Chem Phys 2014; 16:13069-73. [DOI: 10.1039/c4cp01090f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Computational examination of the spontaneous dimerization of Aβ21–30and stability measures of the resulting parallel and anti-parallel aligned dimers.
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Affiliation(s)
| | - J. Srinivasa Rao
- Department of Physics
- New Jersey Institute of Technology
- University Heights
- Newark, USA
| | - Luis Cruz
- Department of Physics
- Drexel University
- Philadelphia, USA
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29
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Irbäck A, Mohanty S. All-Atom Monte Carlo Simulations of Protein Folding and Aggregation. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [DOI: 10.1007/978-3-642-28554-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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30
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Lv Z, Roychaudhuri R, Condron MM, Teplow DB, Lyubchenko YL. Mechanism of amyloid β-protein dimerization determined using single-molecule AFM force spectroscopy. Sci Rep 2013; 3:2880. [PMID: 24096987 PMCID: PMC3791449 DOI: 10.1038/srep02880] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/20/2013] [Indexed: 01/27/2023] Open
Abstract
Aβ42 and Aβ40 are the two primary alloforms of human amyloid β−protein (Aβ). The two additional C−terminal residues of Aβ42 result in elevated neurotoxicity compared with Aβ40, but the molecular mechanism underlying this effect remains unclear. Here, we used single−molecule force microscopy to characterize interpeptide interactions for Aβ42 and Aβ40 and corresponding mutants. We discovered a dramatic difference in the interaction patterns of Aβ42 and Aβ40 monomers within dimers. Although the sequence difference between the two peptides is at the C−termini, the N−terminal segment plays a key role in the peptide interaction in the dimers. This is an unexpected finding as N−terminal was considered as disordered segment with no effect on the Aβ peptide aggregation. These novel properties of Aβ proteins suggests that the stabilization of N−terminal interactions is a switch in redirecting of amyloids form the neurotoxic aggregation pathway, opening a novel avenue for the disease preventions and treatments.
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Affiliation(s)
- Zhengjian Lv
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198, United States
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31
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Bille A, Jónsson SÆ, Akke M, Irbäck A. Local unfolding and aggregation mechanisms of SOD1: a Monte Carlo exploration. J Phys Chem B 2013; 117:9194-202. [PMID: 23844996 DOI: 10.1021/jp404500b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Copper, zinc superoxide dismutase 1 (SOD1) is a ubiquitous homodimeric enzyme, whose misfolding and aggregation play a potentially key role in the neurodegenerative disease amyotrophic lateral sclerosis (ALS). SOD1 aggregation is thought to be preceded by dimer dissociation and metal loss, but the mechanisms by which the metal-free monomer aggregates remain incompletely understood. Here we use implicit solvent all-atom Monte Carlo (MC) methods to investigate the local unfolding dynamics of the β-barrel-forming SOD1 monomer. Although event-to-event variations are large, on average, we find clear differences in dynamics among the eight strands forming the β-barrel. Most dynamic is the eighth strand, β8, which is located in the dimer interface of native SOD1. For the four strands in or near the dimer interface (β1, β2, β7, and β8), we perform aggregation simulations to assess the propensity of these chain segments to self-associate. We find that β1 and β2 readily self-associate to form intermolecular parallel β-sheets, whereas β8 shows a very low aggregation propensity.
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Affiliation(s)
- Anna Bille
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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32
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Lovas S, Zhang Y, Yu J, Lyubchenko YL. Molecular mechanism of misfolding and aggregation of Aβ(13-23). J Phys Chem B 2013; 117:6175-86. [PMID: 23642026 DOI: 10.1021/jp402938p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The misfolding and self-assembly of the amyloid-beta (Aβ) peptide into aggregates is a molecular signature of the development of Alzheimer's disease, but molecular mechanisms of the peptide aggregation remain unknown. Here, we combined Atomic Force Microscopy (AFM) and Molecular Dynamics (MD) simulations to characterize the misfolding process of an Aβ peptide. Dynamic force spectroscopy AFM analysis showed that the peptide forms stable dimers with a lifetime of ∼1 s. During MD simulations, isolated monomers gradually adopt essentially similar nonstructured conformations independent from the initial structure. However, when two monomers approach their structure changes dramatically, and the conformational space for the two monomers become restricted. The arrangement of monomers in antiparallel orientation leads to the cooperative formation of β-sheet conformation. Interactions, including hydrogen bonds, salt bridges, and weakly polar interactions of side chains stabilize the structure of the dimer. Under the applied force, the dimer, as during the AFM experiments, dissociates in a cooperative manner. Thus, misfolding of the Aβ peptide proceeds via the loss of conformational flexibility and formation of stable dimers suggesting their key role in the subsequent Aβ aggregation process.
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Affiliation(s)
- Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, United States.
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33
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Zhang T, Zhang J, Derreumaux P, Mu Y. Molecular mechanism of the inhibition of EGCG on the Alzheimer Aβ(1-42) dimer. J Phys Chem B 2013; 117:3993-4002. [PMID: 23537203 DOI: 10.1021/jp312573y] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Growing evidence supports that amyloid β (Aβ) oligomers are the major causative agents leading to neural cell death in Alzheimer's disease. The polyphenol (-)-epigallocatechin gallate (EGCG) was recently reported to inhibit Aβ fibrillization and redirect Aβ aggregation into unstructured, off-pathway oligomers. Given the experimental challenge to characterize the structures of Aβ/EGCG complexes, we performed extensive atomistic replica exchange molecular dynamics simulations of Aβ1-42 dimer in the present and absence of EGCG in explicit solvent. Our equilibrium Aβ dimeric structures free of EGCG are consistent with the collision cross section from ion-mobility mass spectrometry and the secondary structure composition from circular dichroism experiment. In the presence of EGCG, the Aβ structures are characterized by increased inter-center-of-mass distances, reduced interchain and intrachain contacts, reduced β-sheet content, and increased coil and α-helix contents. Analysis of the free energy surfaces reveals that the Aβ dimer with EGCG adopts new conformations, affecting therefore its propensity to adopt fibril-prone states. Overall, this study provides, for the first time, insights on the equilibrium structures of Aβ1-42 dimer in explicit aqueous solution and an atomic picture of the EGCG-mediated conformational change on Aβ dimer.
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Affiliation(s)
- Tong Zhang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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34
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Ly S, Altman R, Petrlova J, Lin Y, Hilt S, Huser T, Laurence TA, Voss JC. Binding of apolipoprotein E inhibits the oligomer growth of amyloid-β peptide in solution as determined by fluorescence cross-correlation spectroscopy. J Biol Chem 2013; 288:11628-35. [PMID: 23430745 DOI: 10.1074/jbc.m112.411900] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the primary neuropathological hallmarks of Alzheimer disease is the presence of extracellular amyloid plaques resulting from the aggregation of amyloid-β (Aβ) peptides. The intrinsic disorder of the Aβ peptide drives self-association and progressive reordering of the conformation in solution, and this dynamic distribution of Aβ complicates biophysical studies. This property poses a challenge for understanding the interaction of Aβ with apolipoprotein E (apoE). ApoE plays a pivotal role in the aggregation and clearance of Aβ peptides in the brain, and the ε4 allele of APOE is the most significant known genetic modulator of Alzheimer risk. Understanding the interaction between apoE and Aβ will provide insight into the mechanism by which different apoE isoforms determine Alzheimer disease risk. Here we applied alternating laser excitation fluorescence cross-correlation spectroscopy to observe the single molecule interaction of Aβ with apoE in the hydrated state. The diffusion time of freely diffusing Aβ in the absence of apoE shows significant self-aggregation, whereas in the presence of apoE, binding of the protein results in a more stable complex. These results show that apoE slows down the oligomerization of Aβ in solution and provide direct insight into the process by which apoE influences the deposition and clearance of Aβ peptides in the brain. Furthermore, by developing an approach to remove signals arising from very large Aβ aggregates, we show that real-time single particle observations provide access to information regarding the fraction of apoE bound and the stoichiometry of apoE and Aβ in the complex.
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Affiliation(s)
- Sonny Ly
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
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35
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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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36
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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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37
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Zhao LN, Long H, Mu Y, Chew LY. The toxicity of amyloid β oligomers. Int J Mol Sci 2012; 13:7303-7327. [PMID: 22837695 PMCID: PMC3397527 DOI: 10.3390/ijms13067303] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 12/13/2022] Open
Abstract
In this review, we elucidate the mechanisms of Aβ oligomer toxicity which may contribute to Alzheimer's disease (AD). In particular, we discuss on the interaction of Aβ oligomers with the membrane through the process of adsorption and insertion. Such interaction gives rises to phase transitions in the sub-structures of the Aβ peptide from α-helical to β-sheet structure. By means of a coarse-grained model, we exhibit the tendency of β-sheet structures to aggregate, thus providing further insights to the process of membrane induced aggregation. We show that the aggregated oligomer causes membrane invagination, which is a precursor to the formation of pore structures and ion channels. Other pathological progressions to AD due to Aβ oligomers are also covered, such as their interaction with the membrane receptors, and their direct versus indirect effects on oxidative stress and intraneuronal accumulation. We further illustrate that the molecule curcumin is a potential Aβ toxicity inhibitor as a β-sheet breaker by having a high propensity to interact with certain Aβ residues without binding to them. The comprehensive understanding gained from these current researches on the various toxicity mechanisms show promises in the provision of better therapeutics and treatment strategies in the near future.
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Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
| | - HonWai Long
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
- High Performance Computing Centre, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Lock Yue Chew
- School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637731, Singapore; E-Mails: (L.N.Z.); (H.W.L.)
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38
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Jónsson SAE, Mohanty S, Irbäck A. Distinct phases of free α-synuclein-A Monte Carlo study. Proteins 2012; 80:2169-77. [DOI: 10.1002/prot.24107] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 04/16/2012] [Accepted: 04/25/2012] [Indexed: 11/07/2022]
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39
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Impact of chemical heterogeneity on protein self-assembly in water. Proc Natl Acad Sci U S A 2012; 109:7636-41. [PMID: 22538814 DOI: 10.1073/pnas.1120646109] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hydrophobicity is thought to underlie self-assembly in biological systems. However, the protein surface comprises hydrophobic and hydrophilic patches, and understanding the impact of such a chemical heterogeneity on protein self-assembly in water is of fundamental interest. Here, we report structural and thermodynamic investigations on the dimer formation of full-length amyloid-β proteins in water associated with Alzheimer's disease. Spontaneous dimerization process--from the individual diffusive regime at large separations, through the approach stage in which two proteins come close to each other, to the structural adjustment stage toward compact dimer formation--was captured in full atomic detail via unguided, explicit-water molecular dynamics simulations. The integral-equation theory of liquids was then applied to simulated protein structures to analyze hydration thermodynamic properties and the water-mediated interaction between proteins. We demonstrate that hydrophilic residues play a key role in initiating the dimerization process. A long-range hydration force of enthalpic origin acting on the hydrophilic residues provides the major thermodynamic force that drives two proteins to approach from a large separation to a contact distance. After two proteins make atomic contacts, the nature of the water-mediated interaction switches from a long-range enthalpic attraction to a short-range entropic one. The latter acts both on the hydrophobic and hydrophilic residues. Along with the direct protein-protein interactions that lead to the formation of intermonomer hydrogen bonds and van der Waals contacts, the water-mediated attraction of entropic origin brings about structural adjustment of constituent monomer proteins toward the formation of a compact dimer structure.
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40
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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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41
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Côté S, Laghaei R, Derreumaux P, Mousseau N. Distinct dimerization for various alloforms of the amyloid-beta protein: Aβ(1-40), Aβ(1-42), and Aβ(1-40)(D23N). J Phys Chem B 2012; 116:4043-55. [PMID: 22409719 DOI: 10.1021/jp2126366] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Amyloid-beta protein is related to Alzheimer's disease, and various experiments have shown that oligomers as small as the dimer are cytotoxic. Two alloforms are mainly produced: Aβ(1-40) and Aβ(1-42). They have very different oligomer distributions, and it was recently suggested, from experimental studies, that this variation may originate from structural differences in their dimer structures. Little structural information is available on the Aβ dimer, however, and to complement experimental observations, we simulated the folding of the wild-type Aβ(1-40) and Aβ(1-42) dimers as well as the mutated Aβ(1-40)(D23N) dimer using an accurate coarse-grained force field coupled to Hamiltonian-temperature replica exchange molecular dynamics. The D23N variant impedes the salt-bridge formation between D23 and K28 seen in the wild-type Aβ, leading to very different fibrillation properties and final amyloid fibrils. Our results show that the Aβ(1-42) dimer has a higher propensity than the Aβ(1-40) dimer to form β-strands at the central hydrophobic core (residues 17-21) and at the C-terminal (residues 30-42), which are two segments crucial to the oligomerization of Aβ. The free energy landscape of the Aβ(1-42) dimer is also broader and more complex than that of the Aβ(1-40) dimer. Interestingly, D23N also impacts the free energy landscape by increasing the population of configurations with higher β-strand propensities when compared against Aβ(40). In addition, while Aβ(1-40)(D23N) displays a higher β-strand propensity at the C-terminal, its solvent accessibility does not change with respect to the wild-type sequence. Overall, our results show the strong impact of the two amino acids Ile41-Ala42 and the salt-bridge D23-K28 on the folding of the Aβ dimer.
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Affiliation(s)
- Sébastien Côté
- Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, Montréal, Québec, Canada
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42
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Chebaro Y, Jiang P, Zang T, Mu Y, Nguyen PH, Mousseau N, Derreumaux P. Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure. J Phys Chem B 2012; 116:8412-22. [PMID: 22283547 DOI: 10.1021/jp2118778] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The amyloid-β protein (Aβ) oligomers are believed to be the main culprits in the cytoxicity of Alzheimer's disease (AD) and p3 peptides (Aβ17-42 fragments) are present in AD amyloid plaques. Many small-molecule or peptide-based inhibitors are known to slow down Aβ aggregation and reduce the toxicity in vitro, but their exact modes of action remain to be determined since there has been no atomic level of Aβ(p3)-drug oligomers. In this study, we have determined the structure of Aβ17-42 trimers both in aqueous solution and in the presence of five small-molecule inhibitors using a multiscale computational study. These inhibitors include 2002-H20, curcumin, EGCG, Nqtrp, and resveratrol. First, we used replica exchange molecular dynamics simulations coupled to the coarse-grained (CG) OPEP force field. These CG simulations reveal that the conformational ensemble of Aβ17-42 trimer can be described by 14 clusters with each peptide essentially adopting turn/random coil configurations, although the most populated cluster is characterized by one peptide with a β-hairpin at Phe19-Leu31. Second, these 14 dominant clusters and the less-frequent fibril-like state with parallel register of the peptides were subjected to atomistic Autodock simulations. Our analysis reveals that the drugs have multiple binding modes with different binding affinities for trimeric Aβ17-42 although they interact preferentially with the CHC region (residues 17-21). The compounds 2002-H20 and Nqtrp are found to be the worst and best binders, respectively, suggesting that the drugs may interfere at different stages of Aβ oligomerization. Finally, explicit solvent molecular dynamics of two predicted Nqtrp-Aβ17-42 conformations describe at atomic level some possible modes of action for Nqtrp.
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Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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43
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Chong SH, Ham S. Atomic-level investigations on the amyloid-β dimerization process and its driving forces in water. Phys Chem Chem Phys 2012; 14:1573-5. [DOI: 10.1039/c2cp23326f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Tuffery P, Derreumaux P. Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface 2011; 9:20-33. [PMID: 21993006 DOI: 10.1098/rsif.2011.0584] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The recognition process between a protein and a partner represents a significant theoretical challenge. In silico structure-based drug design carried out with nothing more than the three-dimensional structure of the protein has led to the introduction of many compounds into clinical trials and numerous drug approvals. Central to guiding the discovery process is to recognize active among non-active compounds. While large-scale computer simulations of compounds taken from a library (virtual screening) or designed de novo are highly desirable in the post-genomic area, many technical problems remain to be adequately addressed. This article presents an overview and discusses the limits of current computational methods for predicting the correct binding pose and accurate binding affinity. It also presents the performances of the most popular algorithms for exploring binary and multi-body protein interactions.
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Affiliation(s)
- Pierre Tuffery
- INSERM UMR-S 973, Université Paris Diderot, 35 rue Hélène Brion, 75251 Paris cedex, France
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Zhao LN, Chiu SW, Benoit J, Chew LY, Mu Y. Amyloid β Peptides Aggregation in a Mixed Membrane Bilayer: A Molecular Dynamics Study. J Phys Chem B 2011; 115:12247-56. [DOI: 10.1021/jp2065985] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - See-Wing Chiu
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jérôme Benoit
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Lock Yue Chew
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Jónsson SÆ, Mohanty S, Irbäck A. Accelerating atomic-level protein simulations by flat-histogram techniques. J Chem Phys 2011; 135:125102. [DOI: 10.1063/1.3643328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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