Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data

Torsten John; Lisandra L Martin; Herre Jelger Risselada; Bernd Abel

doi:10.1016/j.dib.2022.108598

Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data

Data Brief. 2022 Sep 14:45:108598. doi: 10.1016/j.dib.2022.108598. eCollection 2022 Dec.

Authors

Torsten John^{1

2

3}, Lisandra L Martin³, Herre Jelger Risselada^{1

4}, Bernd Abel^{1

2}

Affiliations

¹ Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany.
² Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany.
³ School of Chemistry, Monash University, Clayton, Victoria 3800, Australia.
⁴ Institute for Theoretical Physics, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany.

Abstract

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.

Keywords: Aggregation; Amyloid; Aß40, amyloid beta (1–40); Curvature; MD, molecular dynamics; Nanoparticle; Oligomer; PBC, periodic boundary conditions; PDB, protein data bank; Peptide; SPC, simple point charge; Self-assembly; Size.