Molecular Dynamics Trajectories Exploring the Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution

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)本数据集对应de Bruyn、Dorn、Rossetti、Fernandez、Outeiro、Schulz与Carloni的研究论文《磷酸化对水溶液中人α-突触核蛋白生理构象的影响》（Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution），该稿件已提交至《化学信息与建模期刊》（Journal of Chemical Information and Modeling）。 本数据集包含32个复本（温度区间为300~500 K，采用REST2算法（REST2）进行复本交换，Wang等人2011年研究）中温度最低的300 K复本的所有GROMACS输入文件、参数化拓扑文件、初始与最终构型以及分子动力学轨迹。数据分为三个压缩包： 1. all_atom_trajectories.zip：包含所有输入文件与含溶剂的全原子轨迹，轨迹采样间隔为100 ps。 2. protein+ion_trajectories.zip：包含不含溶剂但含离子的构型/非参数化拓扑文件与轨迹，轨迹采样间隔为10 ps。 3. additional_simulations.zip：包含论文补充材料中额外模拟的全原子轨迹、输入文件，以及上述不含溶剂的轨迹；该压缩包涵盖两类模拟：基于DES-Amber力场（Tucker等人2022年研究）的64个复本（温度区间300~600 K）模拟，以及基于a99SB-disp力场的模拟。 顶层文件夹命名规则如下： - DES-Amber simulations/：采用DES-Amber力场完成的模拟（Tucker等人2022年研究） - a99SB-disp simulations/：采用针对内在无序蛋白（Intrinsically Disordered Proteins, IDPs）开发的a99SB-disp力场完成的模拟（Robustelli等人2018年研究） 子文件夹命名规则如下： - AS/：野生型人α-突触核蛋白生理构象的模拟 - unphosphorylated：未磷酸化的野生型人α-突触核蛋白生理构象模拟 - pAS/：S129位点磷酸化且带双负电荷的野生型人α-突触核蛋白生理构象的模拟 - pASH/：仅针对a99SB-disp模拟的、S129位点磷酸化且带单负电荷（单质子化）的野生型人α-突触核蛋白生理构象的模拟