ArticleBiophysical journal2004
Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Structural diversity of Alzheimer's disease amyloid-β dimers and their role in oligomerization and fibril formation.Journal of Alzheimer's disease : JAD · 2014Article
- An effective solvent theory connecting the underlying mechanisms of osmolytes and denaturants for protein stability.Biophysical journal · 2011Article
- Toward a molecular theory of early and late events in monomer to amyloid fibril formation.Annual review of physical chemistry · 2011Review
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- Protein folding: then and now.Archives of biochemistry and biophysics · 2008Article
- The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.Biophysical journal · 2006Article
- Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation.Biophysical journal · 2006Article
- Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations.Journal of the American Chemical Society · 2006Article
- Frequencies of hydrophobic and hydrophilic runs and alternations in proteins of known structure.Protein science : a publication of the Protein Society · 2006Article
- Coarse-grained strategy for modeling protein stability in concentrated solutions.Biophysical journal · 2005Article
- The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent.Biophysical journal · 2005Article
- Phase diagrams describing fibrillization by polyalanine peptides.Biophysical journal · 2004Article
- Oligomerization of amyloid Abeta16-22 peptides using hydrogen bonds and hydrophobicity forces.Biophysical journal · 2004Article
- Sampling the self-assembly pathways of KFFE hexamers.Biophysical journal · 2004Article
- Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations.Biophysical journal · 2004Article
- Thermodynamics and stability of a beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models.Protein science : a publication of the Protein Society · 2004Article
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3 authors.
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Abstract
We have performed discontinuous molecular dynamic simulations of the assembly and folding kinetics of a tetrameric beta-sheet complex that contains four identical four-stranded antiparallel beta-sheet peptides. The potential used in the simulation is a hybrid Go-type potential characterized by the bias gap parameter g, an artificial measure of a model protein's preference for its native state, and the intermolecular contact parameter eta, which measures the ratio of intermolecular to intramolecular native attractions. The formation of the beta-sheet complex and its equilibrium properties strongly depend on the size of the intermolecular contact parameter eta. The ordered beta-sheet complex in the folded state and nonaligned beta-sheets or tangled chains in the misfolded state are distinguished by measuring the squared radius of gyration Rg2 and the fraction of native contacts Q. The folding yield for the folded state is high at intermediate values of eta, but is low at both small and large values of eta. The folded state at small eta is liquid-like, but is solid-like at both intermediate and large eta. The misfolded state at small eta contains nonaligned beta-sheets and tangled chains with poor secondary structure at large eta. Various folding pathways via dimeric and trimeric intermediates are observed, depending on eta. Comparison with experimental results on protein aggregation indicates that intermediate eta values are most appropriate for modeling fibril formation and small eta values are most appropriate for modeling the formation of amorphous aggregates.
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