Dataset

FZJ-2024-06869

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Molecular Dynamics Trajectories Exploring the Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution

de Bruyn, E. (First author)FZJ*RWTH* ; Dorn, A. (First author)FZJ* ; Rossetti, G. (Corresponding author)FZJ*RWTH* ; Fernandez, C. O. ; Outeiro, T. F. ; Schulz, J. B.FZJ*RWTH* ; Carloni, P. (Last author)FZJ*RWTH*

2024
Forschungszentrum Jülich Jülich

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Please use a persistent id in citations: doi:10.5281/ZENODO.12605635  doi:10.5281/zenodo.12605635

Abstract: Primary data for the publication 'Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution' by de Bruyn, Dorn, Rossetti, Fernandez, Outeiro, Schulz and Carloni. Submitted to the Journal of Chemical Information and Modeling. Included are all GROMACS input files, parameterised topologies, starting and final configurations, and trajectories for the lowest temperature replica (at 300 K, lowest of 32 replicas between 300-500 K exchanging according to the REST2 algorithm (Wang et al. 2011)). The data is split into three archives: all_atom_trajectories.zip contains all input files and all atom trajectories including solvent trajectories written at 100 ps intervals protein+ion_trajectories.zip contains configuration/non-parameterised topologies and trajectories excluding solvent, but including ions trajectories written at 10 ps intervals additional_simulations.zip contains the all atom trajectories and input files, and solvent-free trajectories above, for the additional simulations in the Supplemental Information of the article: includes the DES-Amber-based simulations with 64 replicas between 300-600 K, and a99SB-disp-based simulations   Folders are named according to the following top level scheme: DES-Amber simulations/ Simulations created using the DES-Amber force field (Tucker et al. 2022) a99SB-disp simulations/ SImulations created using the a99SB-disp force field for Intrinsically Disordered Proteins (IDPs) (Robustelli et al. 2018) Sub-folders follow the following scheme: AS/ Simulations of the physiological form of wild-type Human α-Synuclein unphosphorylated pAS/ Simulations of the physiological form of wild-type Human α-Synuclein phosphorylated at S129 with double negative charge pASH/ Simulations of the physiological form of wild-type Human α-Synuclein (a99SB-disp simulations only) phosphorylated at S129 with a single negative charge (monoprotonated)

Keyword(s): Structural biology ; Biophysics ; PTM ; Phosphorylated Proteins ; Phosphorylation ; aSyn ; AS ; Alpha-Synuclein ; Molecular Dynamics

Note: Published under the Creative Commons Attribution 4.0 International license.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. Computational Biomedicine (INM-9)
3. Jara-Institut Quantum Information (INM-11)

Research Program(s):

1. 5111 - Domain-Specific Simulation & Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) (POF4-511)
2. 5112 - Cross-Domain Algorithms, Tools, Methods Labs (ATMLs) and Research Groups (POF4-511) (POF4-511)
3. DFG project G:(GEPRIS)390729940 - EXC 2067: Multiscale Bioimaging: Von molekularen Maschinen zu Netzwerken erregbarer Zellen (390729940) (390729940)
4. HDS LEE - Helmholtz School for Data Science in Life, Earth and Energy (HDS LEE) (HDS-LEE-20190612) (HDS-LEE-20190612)
5. SFB 1286 B08 - Definition von Kaskaden molekularer Veränderungen bei Synucleinopathien während der Neurodegeneration (B08) (386961151) (386961151)

Appears in the scientific report 2024

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