ArticleProceedings of the National Academy of Sciences of the United States of America2016
Exploring the aggregation free energy landscape of the amyloid-β protein (1-40).
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 136 citations in OpenAlex.
- Amyloid fibril polymorphism: Structural mechanisms of assembly and the links to disease.Current opinion in structural biology · 2026Review
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Epigallocatechin Gallate as a State-Dependent Modulator of Amyloid-Biomolecules · 2026Review
- Submolecular Resolution of β‑Sheet Plasticity: Decoding Mutations and PTMs in Protein Aggregation Disorders.ACS central science · 2025Article
- Exploring Abeta42 monomer diffusion dynamics on fibril surfaces through molecular simulations.Protein science : a publication of the Protein Society · 2025Article
- Generating the polymorph landscapes of amyloid fibrils using AI: RibbonFold.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation.Computational and structural biotechnology journal · 2024Article
- Production of Distinct Fibrillar, Oligomeric, and Other Aggregation States from Network Models of Multibody Interaction.Journal of chemical theory and computation · 2024Article
- Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin's Regulation on Actin Filaments.The journal of physical chemistry. B · 2024Article
- A turn for the worse: Aβ β-hairpins in Alzheimer's disease.Bioorganic & medicinal chemistry · 2024Review
- Genetic Algorithm for Automated Parameterization of Network Hamiltonian Models of Amyloid Fibril Formation.The journal of physical chemistry. B · 2024Article
- The elementary reactions for incorporation into crystals.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Nucleation of α-Synuclein Amyloid Fibrils Induced by Cross-Interaction with β-Hairpin Peptides Derived from Immunoglobulin Light Chains.International journal of molecular sciences · 2023Article
- Neural potentials of proteins extrapolate beyond training data.The Journal of chemical physics · 2023Article
- Integrative modeling of diverse protein-peptide systems using CABS-dock.PLoS computational biology · 2023Article
- Machine learned coarse-grained protein force-fields: Are we there yet?Current opinion in structural biology · 2023Review
- Early-Stage Oligomerization of Prion-like Polypeptides Reveals the Molecular Mechanism of Amyloid-Disrupting Capacity by Proline Residues.The journal of physical chemistry. B · 2023Article
- Free Gangliosides Can Alter Amyloid-β Aggregation.The journal of physical chemistry letters · 2022Article
- Folding Mechanism and Aggregation Propensity of the KH0 Domain of FMRP and Its R138Q Pathological Variant.International journal of molecular sciences · 2022Article
- Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
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Authors and funding
4 authors at 2 institutions in 1 country.
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Abstract
A predictive coarse-grained protein force field [associative memory, water-mediated, structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the energy landscapes and relative stabilities of amyloid-β protein (1-40) in the monomer and all of its oligomeric forms up to an octamer. We find that an isolated monomer is mainly disordered with a short α-helix formed at the central hydrophobic core region (L17-D23). A less stable hairpin structure, however, becomes increasingly more stable in oligomers, where hydrogen bonds can form between neighboring monomers. We explore the structure and stability of both prefibrillar oligomers that consist of mainly antiparallel β-sheets and fibrillar oligomers with only parallel β-sheets. Prefibrillar oligomers are polymorphic but typically take on a cylindrin-like shape composed of mostly antiparallel β-strands. At the concentration of the simulation, the aggregation free energy landscape is nearly downhill. We use umbrella sampling along a structural progress coordinate for interconversion between prefibrillar and fibrillar forms to identify a conversion pathway between these forms. The fibrillar oligomer only becomes favored over its prefibrillar counterpart in the pentamer where an interconversion bottleneck appears. The structural characterization of the pathway along with statistical mechanical perturbation theory allow us to evaluate the effects of concentration on the free energy landscape of aggregation as well as the effects of the Dutch and Arctic mutations associated with early onset of Alzheimer's disease.
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