Integrative determination of atomic structure of mutant huntingtin exon 1 fibrils implicated in Huntington disease — data files

This zenodo entry contains MD and solid-state NMR data files for the paper: Mahdi Bagherpoor Helabad et al. (2024) Integrative determination of atomic structure of mutant huntingtin exon 1 fibrils implicated in Huntington disease MD datasets and code We provide here (in MD_simulations_data_codes.zip) the MD simulations files for the MD runs and also data, and their respective codes, shown in the figures of the above papers. Data file structure: MD_data The MD simulation run files for three fully periodic systems—PolyQ15 and HTTex1—include the following: .gro files for both minimization and final structures, production .tpr files, force field parameters, GROMACS .mdp files, and position and dihedral restraint files. fully_periodic_systems polyQ15 HTTex1 Figs_Data_Codes The data and in-house Python scripts associated with creating the figures: Fig2B_S4 for Figure 2B and Supplementary Figure 4 Fig2D_S5 for Figure 2D and Supplementary Figure 5 Fig3C_S10 for Figure 3C and Supplementary Figure 10 Fig4_S12_S13_S14 for Figure 4C and Supplementary Figures 12–14 Fig6C for Figure 6C FigS3B_S6 for Supplementary Figures 3B and 6 FigS8 for Supplementary Figure 8 FigS9_S11 for Supplementary Figures 9–11 FigS16_to_S21 for Supplementary Figures 16–21 FigS22 for Supplementary Figure 22 readMe.txt Fig6_c_barplot_data.xlsx Excel file with data plotted in Figure 6C. N17_SecStr_convergence.xlsx Excel file with convergence data for N17 domain. Solid-state NMR data We provide here the solid-state NMR spectrum files for the data shown in figures of the above paper. Data file structure: SSNMR_data_listing_20241011a.txt text file describing the ssNMR data files SSNMR_data.zip Figure_1 - data for Figure 1F Figure_5 - data for Figure 5 Figure_6 - data for Figure 6 Figure_S7 - data for Figure 2G and Supplementary Figure 7 Figure_S15 - NMR data for HDX ssNMR of fibrils – Supplementary Figure 15 Fig6_b_barplot_data.xlsx Excel file with data plotted in Figure 6B, based on previously reported results (DOI 10.1038/ncomms15462) Data are provided in either Bruker Topspin format, or in NMRPIPE format (ft2 extension). Experimental parameters are described in the published paper and its Supplementary Information files. In general, these are all data from magic-angle-spinning (MAS) NMR studies of intact amyloid fibrils made with isotope labeled HTTex1 fibrils. Experimental types include 2D CP-DARR, 2D TOBSY, 2D HETCOR spectra as well as relaxation measurements. Aside from NMR datafiles, also documents with interpreted and integrated data are included, used to make data curves in the figure (e.g. for Prism software).本Zenodo条目包含对应论文的分子动力学（Molecular Dynamics, MD）与固态核磁共振（Solid-State Nuclear Magnetic Resonance, ssNMR）数据文件，对应论文为： Mahdi Bagherpoor Helabad 等人（2024）《亨廷顿病相关突变亨廷顿蛋白外显子1原纤维原子结构的整合解析》 ## MD 数据集与代码 我们在`MD_simulations_data_codes.zip`中提供了上述论文各配图所用的分子动力学模拟运行文件、配套数据及对应代码。 ### 数据文件结构 #### MD_data 该文件夹包含三个全周期性体系（PolyQ15 与 HTTex1）的分子动力学模拟运行文件，具体包含：用于能量最小化与最终结构的`.gro`文件、生产模拟`.tpr`文件、力场参数文件、GROMACS 仿真配置`.mdp`文件，以及位置与二面角约束文件。 其下子目录结构为： `fully_periodic_systems` ├─ `polyQ15` └─ `HTTex1` #### Figs_Data_Codes 该文件夹包含用于生成论文图表的配套数据与自研 Python 脚本： - `Fig2B_S4`：对应图 2B 与补充图 4 - `Fig2D_S5`：对应图 2D 与补充图 5 - `Fig3C_S10`：对应图 3C 与补充图 10 - `Fig4_S12_S13_S14`：对应图 4C 与补充图 12~14 - `Fig6C`：对应图 6C - `FigS3B_S6`：对应补充图 3B 与补充图 6 - `FigS8`：对应补充图 8 - `FigS9_S11`：对应补充图 9~11 - `FigS16_to_S21`：对应补充图 16~21 - `FigS22`：对应补充图 22 - `readMe.txt`：说明文档 - `Fig6_c_barplot_data.xlsx`：用于绘制图 6C 的 Excel 数据文件 - `N17_SecStr_convergence.xlsx`：包含 N17 结构域收敛性数据的 Excel 文件 ## 固态核磁共振数据 我们提供了上述论文各配图所用的固态核磁共振谱图文件。 ### 数据文件结构 1. `SSNMR_data_listing_20241011a.txt`：描述固态核磁共振数据文件的文本文档 2. `SSNMR_data.zip`：包含以下内容： - `Figure_1`：对应图 1F 的数据 - `Figure_5`：对应图 5 的数据 - `Figure_6`：对应图 6 的数据 - `Figure_S7`：对应图 2G 与补充图 7 的数据 - `Figure_S15`：对应原纤维氢氘交换固态核磁共振的 NMR 数据，即补充图 15 3. `Fig6_b_barplot_data.xlsx`：基于已发表成果（DOI 10.1038/ncomms15462）绘制图 6B 的 Excel 数据文件 所有数据以 Bruker Topspin 格式或 NMRPIPE 格式（后缀为`.ft2`）提供。实验参数详见已发表论文及其补充信息文件。总体而言，所有数据均来自对同位素标记 HTTex1 原纤维的魔角旋转（Magic-Angle Spinning, MAS）核磁共振研究，实验类型涵盖 2D CP-DARR、2D TOBSY、2D HETCOR 谱图以及弛豫测量。除核磁共振数据文件外，还包含用于生成图表数据曲线的解析与整合后数据文档（例如适配 Prism 软件的相关文件）。