ArticleJournal of the American Chemical Society2006
Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations.
Article in Journal of the American Chemical Society, 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.
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.Chemical reviews · 2021Review
- Protein aggregation: in silico algorithms and applications.Biophysical reviews · 2021Review
- A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model.The Journal of chemical physics · 2019Article
- Simulations and Experiments Delineate Amyloid Fibrilization by Peptides Derived from Glaucoma-Associated Myocilin.The journal of physical chemistry. B · 2018Article
- HyRes: a coarse-grained model for multi-scale enhanced sampling of disordered protein conformations.Physical chemistry chemical physics : PCCP · 2017Article
- A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Aggregation of Chameleon Peptides: Implications of α-Helicity in Fibril Formation.The journal of physical chemistry. B · 2016Article
- Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.The Journal of chemical physics · 2013Article
- Structural transitions and oligomerization along polyalanine fibril formation pathways from computer simulations.Proteins · 2012Article
- Size distribution of amyloid nanofibrils.Biophysical journal · 2011Article
- Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation.PLoS computational biology · 2011Article
- Article
- Potential aggregation-prone regions in complementarity-determining regions of antibodies and their contribution towards antigen recognition: a computational analysis.Pharmaceutical research · 2010Article
- Conformational preferences of a 14-residue fibrillogenic peptide from acetylcholinesterase.Biochemistry · 2010Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
- Simulations of nucleation and elongation of amyloid fibrils.The Journal of chemical physics · 2009Article
- A polymer physics perspective on driving forces and mechanisms for protein aggregation.Archives of biochemistry and biophysics · 2008Review
- Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.Biophysical journal · 2007Article
- Characterization of the nucleation barriers for protein aggregation and amyloid formation.HFSP journal · 2007Article
- Protein aggregation in silico.Trends in biotechnology · 2007Review
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2 authors.
Funding
Abstract
Fibrillary protein aggregates rich in beta-sheet structure have been implicated in the pathology of several neurodegenerative diseases. In this work, we investigate the formation of fibrils by performing discontinuous molecular dynamics simulations on systems containing 12 to 96 model Ac-KA(14)K-NH(2) peptides using our newly developed off-lattice, implicit-solvent, intermediate-resolution model, PRIME. We find that, at a low concentration, random-coil peptides assemble into alpha-helices at low temperatures. At intermediate concentrations, random-coil peptides assemble into alpha-helices at low temperatures and large beta-sheet structures at high temperatures. At high concentrations, the system forms beta-sheets over a wide range of temperatures. These assemble into fibrils above a critical temperature which decreases with concentration and exceeds the isolated peptide's folding temperature. At very high temperatures and all concentrations, the system is in a random-coil state. All of these results are in good qualitative agreement with those by Blondelle and co-workers on Ac-KA(14)K-NH(2) peptides. The fibrils observed in our simulations mimic the structural characteristics observed in experiments in terms of the number of sheets formed, the values of the intra- and intersheet separations, and the parallel peptide arrangement within each beta-sheet. Finally, we find that when the strength of the hydrophobic interaction between nonpolar side chains is high compared to the strength of hydrogen bonding, amorphous aggregates, rather than fibrillar aggregates, are formed.
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