ArticleProtein science : a publication of the Protein Society2004
Thermodynamics and stability of a beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models.
Article in Protein science : a publication of the Protein Society, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Insights into the Main Protease of SARS-CoV-2: Thermodynamic Analysis, Structural Characterization, and the Impact of Inhibitors.Analytical chemistry · 2024Article
- Toward a molecular theory of early and late events in monomer to amyloid fibril formation.Annual review of physical chemistry · 2011Review
- Replica exchange simulations of the thermodynamics of Abeta fibril growth.Biophysical journal · 2009Article
- Temperature-induced dissociation of Abeta monomers from amyloid fibril.Biophysical journal · 2008Article
- Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation.Biophysical journal · 2006Article
- Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior.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
- Phase diagrams describing fibrillization by polyalanine peptides.Biophysical journal · 2004Article
- Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models.Biophysical journal · 2004Article
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3 authors.
Funding
Abstract
We have performed discontinuous molecular dynamics simulations of the thermodynamics and stability 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 the preference of a model protein for its native state, and the intermolecular contact parameter eta, which measures the ratio of intermolecular to intramolecular native attractions. Despite the simplicity of the model, a complex set of thermodynamic transitions for the beta-sheet complex is revealed that shows there are three distinct oligomer (partially ordered, ordered, and highly ordered beta-sheet complex) states and four noninteracting monomers phases. The thermodynamic properties of the three oligomer states strongly depend on both the size of the intermolecular contact parameter eta and the temperature. The partially ordered beta-sheet complex is made up of four ordered globules and is observed at intermediate to large eta at high temperatures. The ordered beta-sheet complex contains four native beta-sheets and is located at small to intermediate eta at low temperatures in the phase diagram. The highly ordered beta-sheet complex has fully-stiff beta-sheet strands, the same as the global energy minimum structure, and is observed for all eta at low temperatures.
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