ArticleProceedings of the National Academy of Sciences of the United States of America2020
Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 55 citations in OpenAlex.
- Sequence-encoded conformational biases correlate with self-assembly modes of intrinsically disordered proteins.PNAS nexus · 2026Article
- Competing addition processes give distinct growth regimes in the assembly of 1D filaments.Biophysical journal · 2025Article
- The mechanism of amyloid fibril growth from Φ-value analysis.Nature chemistry · 2025Article
- A tunable affinity fusion tag for protein self-assembly.bioRxiv : the preprint server for biology · 2025Article
- Protein aggregates and biomolecular condensates: implications for human health and disease.Frontiers in molecular biosciences · 2025Review
- Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations.The journal of physical chemistry. B · 2024Review
- Growth kinetics of amyloid-like fibrils: An integrated atomistic simulation and continuum theory approach.PNAS nexus · 2024Article
- Nucleation and Growth of Amyloid Fibrils.The journal of physical chemistry. B · 2023Article
- Direct Observation of Seeded Conformational Conversion of hIAPPJournal of chemical information and modeling · 2023Article
- Distinct growth regimes of α-synuclein amyloid elongation.Biophysical journal · 2023Article
- Beneficial and detrimental effects of non-specific binding during DNA hybridization.Biophysical journal · 2023Article
- Controllable membrane damage by tunable peptide aggregation with albumin.AIChE journal. American Institute of Chemical Engineers · 2022Article
- Nanoscale Infrared Spectroscopy Identifies Parallel to Antiparallel β-Sheet Transformation of Aβ Fibrils.The journal of physical chemistry letters · 2022Article
- Conformational entropy limits the transition from nucleation to elongation in amyloid aggregation.Biophysical journal · 2022Article
- Multi-eGO: An in silico lens to look into protein aggregation kinetics at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Mechanistic Kinetic Model Reveals How Amyloidogenic Hydrophobic Patches Facilitate the Amyloid-β Fibril Elongation.ACS chemical neuroscience · 2022Article
- Protein assembly and crowding simulations.Current opinion in structural biology · 2022Review
- Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease.Current opinion in structural biology · 2022Review
- Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A dissipative pathway for the structural evolution of DNA fibres.Nature chemistry · 2021Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Atomistic description of protein fibril formation has been elusive due to the complexity and long time scales of the conformational search. Here, we develop a multiscale approach combining numerous atomistic simulations in explicit solvent to construct Markov State Models (MSMs) of fibril growth. The search for the in-register fully bound fibril state is modeled as a random walk on a rugged two-dimensional energy landscape defined by β-sheet alignment and hydrogen-bonding states, whereas transitions involving states without hydrogen bonds are derived from kinetic clustering. The reversible association/dissociation of an incoming peptide and overall growth kinetics are then computed from MSM simulations. This approach is applied to derive a parameter-free, comprehensive description of fibril elongation of Aβ
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.