Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data
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 s...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-12-01
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| Series: | Data in Brief |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340922008058 |
| _version_ | 1811310799256289280 |
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| author | Torsten John Lisandra L. Martin Herre Jelger Risselada Bernd Abel |
| author_facet | Torsten John Lisandra L. Martin Herre Jelger Risselada Bernd Abel |
| author_sort | Torsten John |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T10:05:32Z |
| format | Article |
| id | doaj.art-728448e701d94f99978f7c8bde6058fd |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-04-13T10:05:32Z |
| publishDate | 2022-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-728448e701d94f99978f7c8bde6058fd2022-12-22T02:51:06ZengElsevierData in Brief2352-34092022-12-0145108598Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation dataTorsten John0Lisandra L. Martin1Herre Jelger Risselada2Bernd Abel3Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany; School of Chemistry, Monash University, Clayton, Victoria 3800, AustraliaSchool of Chemistry, Monash University, Clayton, Victoria 3800, AustraliaLeibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Institute for Theoretical Physics, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany; Corresponding authors at: Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany.Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany; Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Leipzig University, Linnéstraße 3, 04103 Leipzig, Germany; Corresponding authors at: Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany.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.http://www.sciencedirect.com/science/article/pii/S2352340922008058AggregationSelf-assemblyNanoparticleSizeCurvatureOligomer |
| spellingShingle | Torsten John Lisandra L. Martin Herre Jelger Risselada Bernd Abel Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data Data in Brief Aggregation Self-assembly Nanoparticle Size Curvature Oligomer |
| title | Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data |
| title_full | Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data |
| title_fullStr | Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data |
| title_full_unstemmed | Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data |
| title_short | Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data |
| title_sort | curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data |
| topic | Aggregation Self-assembly Nanoparticle Size Curvature Oligomer |
| url | http://www.sciencedirect.com/science/article/pii/S2352340922008058 |
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