ArticleThe journal of physical chemistry. B2017
High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- K16F/E22F Mutation Promotes Oligomerization and Alters β-Sheet Topology of Aβ16-22 Peptides: Insights from Molecular Dynamics Simulations.ACS chemical neuroscience · 2026Article
- Stability and Dynamics of the N‑Terminal Domain of TDP-43 and the Effect of Point Mutations.ACS omega · 2026Article
- A lattice Monte Carlo model for amyloid fibril formation.Biophysics and physicobiology · 2026Article
- Nucleation dynamics in amyloid-beta dimerization revealed by single-molecule fingerprinting.Cell reports. Physical science · 2025Article
- Aberrant S293 Phosphorylation Drives Oligomerization of Tau Repeat R2: Insights from Molecular Dynamics Simulations.ACS chemical neuroscience · 2025Article
- Bay leaves: the neuroprotective dietary spice via inhibition of amyloid-like aggregation.Metabolic brain disease · 2025Article
- Gymnosperm-specific CYP90Js enable biflavonoid biosynthesis and microbial production of amentoflavone.Nature communications · 2025Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Antidiabetic and Antigout Properties of the Ultrasound-Assisted Extraction of Total Biflavonoids fromAntioxidants (Basel, Switzerland) · 2024Article
- A turn for the worse: Aβ β-hairpins in Alzheimer's disease.Bioorganic & medicinal chemistry · 2024Review
- Molecular Insights into Cu/Zn Metal Response to the Amyloid β-Peptide (1-42).ACS physical chemistry Au · 2024Article
- Self-Aggregating Tau Fragments Recapitulate Pathologic Phenotypes and Neurotoxicity of Alzheimer's Disease in Mice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Inhibition Effect and Molecular Mechanisms of Quercetin on the Aβ42 Dimer: A Molecular Dynamics Simulation Study.ACS omega · 2023Article
- Phosphorylation at Ser289 Enhances the Oligomerization of Tau Repeat R2.Journal of chemical information and modeling · 2023Article
- Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.Biophysics and physicobiology · 2023Article
- Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation.Molecules (Basel, Switzerland) · 2022Review
- Effect of Cholesterol Molecules on Aβ1-42 Wild-Type and Mutants Trimers.Molecules (Basel, Switzerland) · 2022Article
- A Disulfide-Stabilized Aβ that Forms Dimers but Does Not Form Fibrils.Biochemistry · 2022Article
- Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments.Biophysics and physicobiology · 2022Article
- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.Methods in molecular biology (Clifton, N.J.) · 2022Article
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3 authors.
Funding
Abstract
The dimer of the amyloid-β peptide Aβ of 42 residues is the smallest toxic species in Alzheimer's disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn, and AMBERsb14 force fields with the TIP3P water model. On the basis of 144 μs replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties, and small-angle X-ray scattering profiles independent of the force field. There are, however, marked differences in secondary structure, with the AMBERsb14 and CHARMM22* ensembles overestimating the CD-derived helix content, and the OPLS-AA and AMBER99sb-ildn secondary structure contents in agreement with CD data. Also the intramolecular beta-hairpin content spanning residues 17-21 and 30-36 varies between 1.5% and 13%. Overall, there are significant differences in tertiary and quaternary conformations among all force fields, and the key finding, irrespective of the force field, is that the dimer is stabilized by nonspecific interactions, explaining therefore its possible transient binding to multiple cellular partners and, in part, its toxicity.
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