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Author: Risselada, Herre Jelger × Has files: Yes ×

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    Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data
    (Amsterdam [u.a.] : Elsevier, 2022) John, Torsten; Martin, Lisandra L.; Risselada, Herre Jelger; Abel, Bernd
    Nanostructured surfaces are widespread in nature and are being further developed in materials science. This makes them highly relevant for biomolecules, such as peptides. In this data article, we present a curvature model and molecular dynamics (MD) simulation data on the influence of nanoparticle size on the stability of amyloid peptide fibrils related to our research article entitled “Mechanistic insights into the size-dependent effects of nanoparticles on inhibiting and accelerating amyloid fibril formation” (John et al., 2022) [1]. We provide the code to perform MD simulations in GROMACS 4.5.7 software of arbitrarily chosen biomolecule oligomers adsorbed on a curved surface of chosen nanoparticle size. We also provide the simulation parameters and data for peptide oligomers of Aß40, NNFGAIL, GNNQQNY, and VQIYVK. The data provided allows researchers to further analyze our MD simulations and the curvature model allows for a better understanding of oligomeric structures on surfaces.
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    Gold-Induced Fibril Growth: The Mechanism of Surface-Facilitated Amyloid Aggregation
    (Weinheim : Wiley-VCH, 2016) Gladytz, Anika; Abel, Bernd; Risselada, Herre Jelger
    The question of how amyloid fibril formation is influenced by surfaces is crucial for a detailed understanding of the process in vivo. We applied a combination of kinetic experiments and molecular dynamics simulations to elucidate how (model) surfaces influence fibril formation of the amyloid-forming sequences of prion protein SUP35 and human islet amyloid polypeptide. The kinetic data suggest that structural reorganization of the initial peptide corona around colloidal gold nanoparticles is the rate-limiting step. The molecular dynamics simulations reveal that partial physisorption to the surface results in the formation of aligned monolayers, which stimulate the formation of parallel, critical oligomers. The general mechanism implies that the competition between the underlying peptide–peptide and peptide–surface interactions must strike a balance to accelerate fibril formation.