ArticleProteins2013
The stability of cylindrin β-barrel amyloid oligomer models-a molecular dynamics study.
Article in Proteins, 2013. 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.
- Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8.PloS one · 2022Article
- Molecular Dynamics Simulations Reveal the Modulated Mechanism of STING Conformation.Interdisciplinary sciences, computational life sciences · 2021Article
- β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis.International journal of molecular sciences · 2021Review
- Spontaneous Formation of β-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta.Nano today · 2021Article
- Computational Investigation of Gantenerumab and Crenezumab Recognition of Aβ Fibrils in Alzheimer's Disease Brain Tissue.ACS chemical neuroscience · 2020Article
- Structural analyses and force fields comparison for NACore (68-78) and SubNACore (69-77) fibril segments of Parkinson's disease.Journal of molecular modeling · 2020Article
- Structural Insight into the Interactions between Structurally Similar Inhibitors and SIRT6.International journal of molecular sciences · 2020Article
- Anatomy of a selectively coassembled β-sheet peptide nanofiber.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A Novel PEGylated Block Copolymer in New Age Therapeutics for Alzheimer's Disease.Molecular neurobiology · 2019Article
- Distinct Binding Dynamics, Sites and Interactions of Fullerene and Fullerenols with Amyloid-β Peptides Revealed by Molecular Dynamics Simulations.International journal of molecular sciences · 2019Article
- Using correlated motions to determine sufficient sampling times for molecular dynamics.Physical review. E · 2018Article
- Machine learning accelerates MD-based binding pose prediction between ligands and proteins.Bioinformatics (Oxford, England) · 2018Article
- Assemblies of amyloid-β30-36 hexamer and its G33V/L34T mutants by replica-exchange molecular dynamics simulation.PloS one · 2017Article
- Effect of single point mutations in a form of systemic amyloidosis.Protein science : a publication of the Protein Society · 2015Article
- Comparative modeling of hypothetical amyloid pores based on cylindrin.Journal of molecular modeling · 2015Article
- On the lack of polymorphism in Aβ-peptide aggregates derived from patient brains.Protein science : a publication of the Protein Society · 2015Article
- Stability of Iowa mutant and wild type Aβ-peptide aggregates.The Journal of chemical physics · 2014Article
- A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly.The journal of physical chemistry. B · 2014Article
- Article
- Mutations and seeding of amylin fibril-like oligomers.The journal of physical chemistry. B · 2013Article
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2 authors.
Funding
Abstract
Small-soluble amyloid oligomers are believed to play a significant role in the pathology of amyloid diseases. Recently, the atomic structure of a toxic oligomer formed by an 11 residue and its tandem repeat was found to have an out-off register antiparallel β-strands in the shape of a β-barrel. In the present article we investigate the effect of mutations in the hydrophobic cores on the structure and dynamic of the β-barrels using all atom multiple molecular dynamics simulations with an explicit solvent. Extending previous experiments with molecular dynamics simulations we systematically test how stability and formation of cylindrin depends on the interplay between hydrophobicity and steric effects of the core residues. We find that strong hydrophobic interactions between geometrically fitting residues keep the strands (both in register and out-off-register interface) in close proximity, which in turn stabilizes the side-chain and main-chain hydrogen bonds, and the salt bridges on the outer surface along the weak out-of-register interface. Our simulations also indicate presence of water molecules in the hydrophobic interior of the cylindrin β-barrel.Proteins 2013.
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