ArticleBiophysical journal2006
Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 69 citations in OpenAlex.
- Interaction Between Ropivacaine and a Self-Assembling Peptide: A Nanoformulation for Long-Acting Analgesia.International journal of nanomedicine · 2022Article
- Protein aggregation: in silico algorithms and applications.Biophysical reviews · 2021Review
- Functional Amyloids Are the Rule Rather Than the Exception in Cellular Biology.Microorganisms · 2020Review
- A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model.The Journal of chemical physics · 2019Article
- Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations.The Journal of chemical physics · 2018Article
- Effects of macromolecular crowding on amyloid beta (16-22) aggregation using coarse-grained simulations.The journal of physical chemistry. B · 2014Article
- A coarse-grained model for polyglutamine aggregation modulated by amphipathic flanking sequences.Biophysical journal · 2014Article
- Article
- Computational approaches to understanding protein aggregation in neurodegeneration.Journal of molecular cell biology · 2014Review
- Influence of temperature on formation of perfect tau fragment fibrils using PRIME20/DMD simulations.Protein science : a publication of the Protein Society · 2012Article
- Fibrillization propensity for short designed hexapeptides predicted by computer simulation.Journal of molecular biology · 2012Article
- Spontaneous formation of twisted Aβ(16-22) fibrils in large-scale molecular-dynamics simulations.Biophysical journal · 2011Article
- Assessing the contribution of heterogeneous distributions of oligomers to aggregation mechanisms of polyglutamine peptides.Biophysical chemistry · 2011Article
- Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides.Proteins · 2011Article
- Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins.Biophysical journal · 2011Article
- Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations.Journal of molecular graphics & modelling · 2011Article
- Article
- Modulation of polyglutamine conformations and dimer formation by the N-terminus of huntingtin.Journal of molecular biology · 2010Article
- Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization.Journal of molecular biology · 2008Article
- Polyglutamine neurodegeneration: protein misfolding revisited.Trends in neurosciences · 2008Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The pathological manifestation of nine hereditary neurodegenerative diseases is the presence within the brain of aggregates of disease-specific proteins that contain polyglutamine tracts longer than a critical length. To improve our understanding of the processes by which polyglutamine-containing proteins misfold and aggregate, we have conducted molecular dynamics simulations of the aggregation of model polyglutamine peptides. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms, depending on the residue being modeled. The effects of hydrophobicity on the system are studied by varying the strength of the hydrophobic interaction from 12.5% to 5% of the hydrogen-bonding interaction strength. In our simulations, we observe the spontaneous formation of aggregates and annular structures that are made up of beta-sheets starting from random configurations of random coils. This result was interesting because tubular protofibrils were recently found in experiments on polyglutamine aggregation and because of Perutz's prediction that polyglutamine would form water-filled nanotubes.
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Registered trials
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.