1
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Tran TT, Pan F, Tran L, Roland C, Sagui C. The F19W mutation reduces the binding affinity of the transmembrane Aβ 11-40 trimer to the membrane bilayer. RSC Adv 2021; 11:2664-2676. [PMID: 35424222 PMCID: PMC8693879 DOI: 10.1039/d0ra08837d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Alzheimer's disease is linked to the aggregation of the amyloid-β protein (Aβ) of 40 or 42 amino acids. Lipid membranes are known to modulate the rate and mechanisms of the Aβ aggregation. Point mutations in Aβ can alter these rates and mechanisms. In particular, experiments show that F19 mutations influence the aggregation rate, but maintain the fibril structures. Here, we used molecular dynamics simulations to examine the effect of the F19W mutation in the 3Aβ11-40 trimer immersed in DPPC lipid bilayers submerged in aqueous solution. Substituting Phe by its closest (non-polar) aromatic amino acid Trp has a dramatic reduction in binding affinity to the phospholipid membrane (measured with respect to the solvated protein) compared to the wild type: the binding free energy of the protein-DPPC lipid bilayer increases by 40-50 kcal mol-1 over the wild-type. This is accompanied by conformational changes and loss of salt bridges, as well as a more complex free energy surface, all indicative of a more flexible and less stable mutated trimer. These results suggest that the impact of mutations can be assessed, at least partially, by evaluating the interaction of the mutated peptides with the lipid membranes.
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Affiliation(s)
- Thanh Thuy Tran
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Feng Pan
- Department of Statistics, Florida State University Tallahassee Florida USA
| | - Linh Tran
- Institute of Fundamental and Applied Sciences, Duy Tan University Ho Chi Minh City 700000 Vietnam
- Faculty of Natural Sciences, Duy Tan University Da Nang City 550000 Vietnam
| | - Christopher Roland
- Department of Physics, North Carolina State University Raleigh North Carolina USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University Raleigh North Carolina USA
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2
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Minh Hung H, Nguyen MT, Tran PT, Truong VK, Chapman J, Quynh Anh LH, Derreumaux P, Vu VV, Ngo ST. Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ 40 Peptide. J Chem Inf Model 2020; 60:1399-1408. [PMID: 32105466 DOI: 10.1021/acs.jcim.9b01074] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is experimental evidence that the astaxanthin, betanin, and epigallocatechin-3-gallate (EGCG) compounds slow down the aggregation kinetics and the toxicity of the amyloid-β (Aβ) peptide. How these inhibitors affect the self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamic (REMD) simulations in an explicit solvent of the Aβ11-40 trimer from the U-shape conformation and MD simulations starting from Aβ1-40 dimer and tetramer structures characterized by different intra- and interpeptide conformations. We find that the three ligands have similar binding free energies on small Aβ40 oligomers but very distinct transient binding sites that will affect the aggregation of larger assemblies and fibril elongation of the Aβ40 peptide.
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Affiliation(s)
- Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Minh Tho Nguyen
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Phuong-Thao Tran
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, Hanoi 100000, Vietnam
| | - Vi Khanh Truong
- School of Science, RMIT University, GPO Box 2476, Melbourne 3001, Australia
| | - James Chapman
- School of Science, RMIT University, GPO Box 2476, Melbourne 3001, Australia
| | - Le Huu Quynh Anh
- Department of Climate Change and Renewable Energy, Ho Chi Minh City University of Natural Resources and Environment, Ho Chi Minh City 700000, Vietnam
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Laboratoire de Biochimie Théorique, UPR9080, CNRS, Université de Paris, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
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3
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Ngo ST, Nguyen PH, Derreumaux P. Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation. J Phys Chem B 2020; 124:617-626. [PMID: 31931566 DOI: 10.1021/acs.jpcb.9b10982] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The aggregation of the amyloid (Aβ) peptide of 39-43 amino acids into plaques is observed in the brain of Alzheimer's disease (AD) patients, but the mechanisms underlying the neurotoxicity of Aβ oligomers are still elusive. One suggested initial mechanism is related to the implications of amyloid membrane interactions, but characterization of these assemblies is challenging by experimental means. In this study, we have explored the stability of a trimer of Aβ11-40 in parallel and antiparallel β-sheet structures for the wild-type sequence and its F20W mutant in a dipalmitoylphosphatidylcholine membrane using atomistic replica exchange molecular dynamic simulations. We show that both the U-shape organization and the assembly of β-hairpins are maintained in the membrane and are resistant to the mutation F20W. In contrast the models are destabilized by the F19P mutation. Overall, our results indicate that these two assemblies represent minimal seeds or nuclei for the formation of either amyloid fibrils, a variety of β-barrel pores, or various aggregates for many Aβ sequences in a membrane-mimicking environment.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,Faculty of Applied Sciences , Ton Duc Thang University , Ho Chi Minh City , Vietnam
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique , UPR 9080, CNRS, Université de Paris , 13 rue Pierre et Marie Curie , 75005 , Paris , France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University , 75005 Paris , France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,Faculty of Pharmacy , Ton Duc Thang University , Ho Chi Minh City , Vietnam
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4
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Taricska N, Horváth D, Menyhárd DK, Ákontz-Kiss H, Noji M, So M, Goto Y, Fujiwara T, Perczel A. The Route from the Folded to the Amyloid State: Exploring the Potential Energy Surface of a Drug-Like Miniprotein. Chemistry 2019; 26:1968-1978. [PMID: 31647140 PMCID: PMC7028080 DOI: 10.1002/chem.201903826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Indexed: 12/16/2022]
Abstract
The amyloid formation of the folded segment of a variant of Exenatide (a marketed drug for type‐2 diabetes mellitus) was studied by electronic circular dichroism (ECD) and NMR spectroscopy. We found that the optimum temperature for E5 protein amyloidosis coincides with body temperature and requires well below physiological salt concentration. Decomposition of the ECD spectra and its barycentric representation on the folded‐unfolded‐amyloid potential energy surface allowed us to monitor the full range of molecular transformation of amyloidogenesis. We identified points of no return (e.g.; T=37 °C, pH 4.1, cE5=250 μm, cNaCl=50 mm, t>4–6 h) that will inevitably gravitate into the amyloid state. The strong B‐type far ultraviolet (FUV)‐ECD spectra and an unexpectedly strong near ultraviolet (NUV)‐ECD signal (Θ≈275–285
nm) indicate that the amyloid phase of E5 is built from monomers of quasi‐elongated backbone structure (φ≈−145°, ψ≈+145°) with strong interstrand Tyr↔Trp interaction. Misfolded intermediates and the buildup of “toxic” early‐stage oligomers leading to self‐association were identified and monitored as a function of time. Results indicate that the amyloid transition is triggered by subtle misfolding of the α‐helix, exposing aromatic and hydrophobic side chains that may provide the first centers for an intermolecular reorganization. These initial clusters provide the spatial closeness and sufficient time for a transition to the β‐structured amyloid nucleus, thus the process follows a nucleated growth mechanism.
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Affiliation(s)
- Nóra Taricska
- Laboratory of Structural Chemistry and Biology &, MTA-ELTE Protein Modeling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1A, 1117, Budapest, Hungary
| | - Dániel Horváth
- Laboratory of Structural Chemistry and Biology &, MTA-ELTE Protein Modeling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1A, 1117, Budapest, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology &, MTA-ELTE Protein Modeling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1A, 1117, Budapest, Hungary
| | - Hanna Ákontz-Kiss
- Laboratory of Structural Chemistry and Biology &, MTA-ELTE Protein Modeling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1A, 1117, Budapest, Hungary
| | - Masahiro Noji
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - András Perczel
- Laboratory of Structural Chemistry and Biology &, MTA-ELTE Protein Modeling Research Group, Eötvös Loránd University, Pázmány Péter sétány 1A, 1117, Budapest, Hungary
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5
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Tung N, Derreumaux P, Vu VV, Nam PC, Ngo ST. C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ 11-42 Tetramer in Solution: Intensive MD Study. ACS OMEGA 2019; 4:11066-11073. [PMID: 31460204 PMCID: PMC6648102 DOI: 10.1021/acsomega.9b00992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
Amyloid beta (Aβ) peptides are characterized as the major factors associated with neuron death in Alzheimer's disease, which is listed as the most common form of neurodegeneration. Disordered Aβ peptides are released from proteolysis of the amyloid precursor protein. The Aβ self-assembly process roughly takes place via five steps: disordered forms → oligomers → photofibrils → mature fibrils → plaques. Although Aβ fibrils are often observed in patient brains, oligomers were recently indicated to be major neurotoxic elements. In this work, the neurotoxic compound S-shape Aβ11-42 tetramer (S4Aβ11-42) was investigated over 10 μs of unbiased MD simulations. In particular, the S4Aβ11-42 oligomer adopted a high dynamics structure, resulting in unsuccessful determination of their structures in experiments. The C-terminal was suggested as the possible nucleation of the Aβ42 aggregation. The sequences 27-35 and 39-40 formed rich β-content, whereas other residues mostly adopted coil structures. The mean value of the β-content over the equilibrium interval is ∼42 ± 3%. Furthermore, the dissociation free energy of the S4Aβ11-42 peptide was predicted using a biased sampling method. The obtained free energy is ΔG US = -58.44 kcal/mol which is roughly the same level as the corresponding value of the U-shape Aβ17-42 peptide. We anticipate that the obtained S4Aβ11-42 structures could be used as targets for AD inhibitor screening over the in silico study.
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Affiliation(s)
- Nguyen
Thanh Tung
- Institute
of Materials Science, Vietnam Academy of
Science and Technology, Hanoi 10307, Vietnam
| | - Philippe Derreumaux
- Laboratory of Theoretical and Chemistry, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty
of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Van V. Vu
- NTT
Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Pham Cam Nam
- Department
of Chemical Engineering, The University
of Da Nang—University of Science and Technology, Da Nang City 550000, Vietnam
| | - Son Tung Ngo
- Laboratory
of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang
University, Ho Chi
Minh City 758307, Vietnam
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6
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Ngo ST, Derreumaux P, Vu VV. Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca2+ Ions. J Phys Chem B 2019; 123:2645-2653. [DOI: 10.1021/acs.jpcb.8b10792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris, 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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7
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Ngo ST, Vu KB, Bui LM, Vu VV. Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method. ACS OMEGA 2019; 4:3887-3893. [PMID: 31459599 PMCID: PMC6648447 DOI: 10.1021/acsomega.8b03258] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
The binding between two biomolecules is one of the most critical factors controlling many bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free binding energy between two biomolecules. In this work, we have demonstrated that the binding affinity of ligands to proteins can be determined through biased sampling simulations. The umbrella sampling (US) method was applied on 20 protein-ligand complexes, including the cathepsin K (CTSK), type II dehydroquinase (DHQase), heat shock protein 90 (HSP90), and factor Xa (FXa) systems. The ligand-binding affinity was evaluated as the difference between the largest and smallest values of the free-energy curve, which was obtained via a potential of mean force analysis. The calculated affinities differ sizably from the previously reported experimental values, with an average difference of ∼3.14 kcal/mol. However, the calculated results are in good correlation with the experimental data, with correlation coefficients of 0.76, 0.87, 0.96, and 0.97 for CTSK, DHQase, HSP90, and FXa, respectively. Thus, the binding free energy of a new ligand can be reliably estimated using our US approach. Furthermore, the root-mean-square errors (RMSEs) of binding affinity of these systems are 1.13, 0.90, 0.37, and 0.25 kcal/mol, for CTSK, DHQase, HSP90, and FXa, respectively. The small RMSE values indicate the good precision of the biased sampling method that can distinguish the ligands exhibiting similar binding affinities.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical
and Computational Biophysics, Ton Duc Thang
University, Ho Chi Minh City 7000000, Vietnam
- Faculty
of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 7000000, Vietnam
| | - Khanh B. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Le Minh Bui
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
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8
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Ngo ST, Tran-Le PD, Ho GT, Le LQ, Bui LM, Vu BK, Thu Phung HT, Nguyen HD, Vo TS, Vu VV. Interaction of carbohydrate binding module 20 with starch substrates. RSC Adv 2019; 9:24833-24842. [PMID: 35528656 PMCID: PMC9069913 DOI: 10.1039/c9ra01981b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/23/2019] [Indexed: 12/03/2022] Open
Abstract
CBM20s are starch-binding domains found in many amylolytic enzymes, including glucoamylase, alpha-amylase, beta-amylases, and a new family of starch-active polysaccharide monooxygenases (AA13 PMOs). Previous studies of CBM20–substrate interaction only concerned relatively small or soluble amylose molecules, while amylolytic enzymes often work on extended chains of insoluble starch molecules. In this study, we utilized molecular simulation techniques to gain further insights into the interaction of CBM20 with substrates of various sizes via its two separate binding sites, termed as BdS1 and BdS2. Results show that substrate binding at BdS1 involving two conserved tryptophan residues is about 2–4 kcal mol−1 stronger than that at BdS2. CBM20 exhibits about two-fold higher affinity for helical substrates than for the amylose random coils. The affinity for amylose individual double helices does not depend on the helices' length. At least three parallel double helices are required for optimal binding. The binding affinity for a substrate containing 3 or more double helices is ∼−15 kcal mol−1, which is 2–3 kcal mol−1 larger than that for individual double helices. 100 ns molecular dynamics simulations were carried out for the binding of CBM20 to an extended substrate containing 3 layers of 9 60-unit double helices (A3L). A stable conformation of CBM20–A3L was found at BdS1. However, when CBM20 binds A3L viaBdS2, it moves across the surface of the substrate and does not form a stable complex. MD simulations show that small amylose helices are quickly disrupted upon binding to CBM20. Our results provide some important molecular insights into the interactions of CBM20 with starch substrates, which will serve as the basis for further studies of CBM20-containing enzymes, including AA13 PMOs. CBM20 quickly disrupts small helical amylose substrates and exhibits optimal binding affinity when the substrate has three or more parallel double helices.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Giap T. Ho
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Loan Q. Le
- Institute of Tropical Biology
- Vietnam Academy of Science and Technology
- Ho Chi Minh City
- Vietnam
| | - Le Minh Bui
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Bao Khanh Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | | | - Hoang-Dung Nguyen
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
- Institute of Tropical Biology
| | - Thanh-Sang Vo
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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9
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Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study. PLoS One 2018; 13:e0204026. [PMID: 30226897 PMCID: PMC6143259 DOI: 10.1371/journal.pone.0204026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/01/2018] [Indexed: 11/19/2022] Open
Abstract
Oligomerization of amyloid beta (Aβ) peptides has been considered as the crucially causative agent in the development of Alzheimer's disease. Etersalate, a nonsteroidal anti-inflammatory oral drug (United State Food and Drug Administration—Unique Ingredient Identifier: 653GN04T2G) was previously suggested to bind well to proto-fibrils of Aβ peptides in silico. Here, the effect of etersalate on the oligomerization of soluble Aβ16–22 hexamer (6Aβ16–22) were extensively investigated using temperature replica exchange molecular dynamics (REMD) simulations over ~16.8 μs in total for 48 replicas (350 ns per replica). The results reveal that etersalate can enter the inner space or bind on the surface of 6Aβ16–22 conformations, which destabilizes the hexamer. Etersalate was predicted to able to cross the blood brain barrier using prediction of absorption, distribution, metabolism, and excretion—toxicity (preADMET) tools. Overall, although the investigation was performed with the low concentration of trial inhibitor, the obtained results indicate that etersalate is a potential drug candidate for AD through inhibiting formation of Aβ oligomers with the average binding free energy of -11.7 kcal/mol.
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10
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Ngo ST, Hung HM, Hong ND, Tung NT. The influences of E22Q mutant on solvated 3Aβ 11-40 peptide: A REMD study. J Mol Graph Model 2018; 83:122-128. [PMID: 29902674 DOI: 10.1016/j.jmgm.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/03/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
The residue E22 plays a critical role in the aggregation process of Amyloid beta (Aβ) peptides. The effect of E22Q mutant on the shapes of the solvated Aβ11-40 trimer is clarified using a replica exchange molecular dynamics (REMD) simulation employing ∼20.6 μs of MD simulations with 48 disparate replicas. The increase of intramolecular polar contacts and salt bridge between the residue D23 to residues (24-29) was observed. The residual secondary structure of the mutated trimer is shifted in a similar way to the picture observed in previous investigations of F19W mutant. The free energy surface (FES) of the mutated E22Q system has a fewer number of minima in comparison with the wild-type trimer. The optimized shapes of the mutated E22Q form a significant increase in beta structure (47%) and serious decrease in coil content (46%) compared with the wild-type (of 36 and 56%, respectively). The binding affinity of constituting chains to the rest is of -43.7 ± 6.5 kcal/mol, implying that the representative structure of E22Q is more stable than the wild-type one. Furthermore, the E22Q mutant increases the size of stable structures due to larger collision cross section (CCS) and solvent accessible area (SASA). The observed results may enhance the Aβ inhibition throughout the contribution to the knowledge of the Aβ oligomerization/aggregation.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Nam Dao Hong
- University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science and Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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11
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Tam NM, Vu KB, Vu VV, Ngo ST. Influence of various force fields in estimating the binding affinity of acetylcholinesterase inhibitors using fast pulling of ligand scheme. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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12
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Coskuner-Weber O, Uversky VN. Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int J Mol Sci 2018; 19:E336. [PMID: 29364151 PMCID: PMC5855558 DOI: 10.3390/ijms19020336] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.
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Affiliation(s)
- Orkid Coskuner-Weber
- Türkisch-Deutsche Universität, Theoretical and Computational Biophysics Group, Molecular Biotechnology, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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13
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Ngo ST, Thu Phung HT, Vu KB, Vu VV. Atomistic investigation of an Iowa Amyloid-β trimer in aqueous solution. RSC Adv 2018; 8:41705-41712. [PMID: 35558787 PMCID: PMC9091969 DOI: 10.1039/c8ra07615d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/04/2018] [Indexed: 11/21/2022] Open
Abstract
The self-assembly of Amyloid beta (Aβ) peptides are widely accepted to associate with Alzheimer's disease (AD) via several proposed mechanisms. Because Aβ oligomers exist in a complicated environment consisting of various forms of Aβ, including oligomers, protofibrils, and fibrils, their structure has not been well understood. The negatively charged residue D23 is one of the critical residues of the Aβ peptide as it is located in the central hydrophobic domain of the Aβ N-terminal and forms a salt-bridge D23-K28, which helps stabilize the loop domain. In the familial Iowa (D23N) mutant, the total net charge of Aβ oligomers decreases, resulting in the decrease of electrostatic repulsion between D23N Aβ monomers and thus the increase in their self-aggregation rate. In this work, the impact of the D23N mutation on 3Aβ11–40 trimer was characterized utilizing temperature replica exchange molecular dynamics (REMD) simulations. Our simulation reveals that D23N mutation significantly enhances the affinity between the constituting chains in the trimer, increases the β-content (especially in the sequence 21–23), and shifts the β-strand hydrophobic core from crossing arrangement to parallel arrangement, which is consistent with the increase in self-aggregation rate. Molecular docking indicates that the Aβ fibril-binding ligands bind to the D23N and WT forms at different poses. These compounds prefer to bind to the N-terminal β-strand of the D23N mutant trimer, while they mostly bind to the N-terminal loop region of the WT. It is important to take into account the difference in the binding of ligands to mutant and wild type Aβ peptides in designing efficient inhibitors for various types of AD. Amyloid beta peptide oligomers are believed to play key roles in Alzheimer's disease pathogenesis. D23N mutation significantly changes their structure and how they bind potential inhibitors.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Khanh B. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute
- Nguyen Tat Thanh University
- Ho Chi Minh City
- Vietnam
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