Research data supporting: The Heterogeneous Solution Ensemble of the DEAD-box Protein Dhh1 Reveals a Modular Architecture
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Zenodo Dataset (DOI: 10.5281/zenodo.18740247) This repository contains the data to reproduce the results shown in the bioRxiv preprint "The Heterogeneous Solution Ensemble of the DEAD-box Protein Dhh1 Reveals a Modular Architecture" (DOI: 10.64898/2025.12.08.692948). Zip Content The .zip contains two main folders, one for atomistic simulations, and one for Coarse Grained simulations with CALVADOS. Also, in both folders there are results obtained with RanCh modelling. For atomistic simulations, a trajectory files Trajectory.T300xtc is present (1.3$\mu$s long), a production trajectory Trajectory_T300_Production.xtc (1$\mu$s long), together with a structure file <.gro> containing water and ions, a topology file <.top>, an index file <.ndx>. From the analysis, the average profile SaxsProfile.dat computed with Crysol, a PLUMED analysis file Plumed-rerun.dat that returns the timeseries and the free energy surface contained in Colvar.dat and Fes2d-Rg_Rmsd1s2m.dat (along with CA structures of Crystallographic and Canonical in PDB format) and the result of conformational clustering in Clustering.log. For CG simulations, there are four folders , for full-length Dhh1 simulations with Constrained or Flexible core, and for single tails simulations. In the main folder there are a plumed.dat file containing the instructions to compute the SAXS profiles, the force-field parameters in <.csv> format, and the .yaml compatible with the CALVADOS framework. Flex contains the 3 replicas, along with the histograms of the core and the full length $R_g$ histograms, and the averaged SAXS profile. Constrained contains the 44 initial structures, the 44 trajectories and the $R_g$ histograms and the resulting SAXS profile. The two tails' folders contain a long trajectory and the $R_g$ histograms. For modelling, each folder provides the files required by RanCh to generate the random-coil structures, a folder with the $10^4$ generated conformations, files with ensemble statistics and the average profiles. Software version requirement Atomistic GROMACS 2021.4 Plumed 2.8.0 Coarse Grained OpenMM 8.2.0 CALVADOS framework (https://github.com/KULL-Centre/CALVADOS/tree/main) Random Coil modelling Ranch from ATSAS 4.0.0
Zenodo 数据集（DOI: 10.5281/zenodo.18740247） 本存储库包含复现bioRxiv预印本《DEAD盒蛋白Dhh1的异质性溶液系综揭示模块化结构》（DOI: 10.64898/2025.12.08.692948）中展示结果所需的全部数据。 ### 压缩包内容 本压缩包包含两个主要文件夹，分别对应全原子模拟（atomistic simulations）与使用CALVADOS的粗粒度模拟（Coarse Grained simulations），且两个文件夹中均包含通过RanCh建模（RanCh modelling）得到的分析结果。 #### 全原子模拟 该目录下包含以下文件：时长1.3μs的轨迹文件Trajectory.T300xtc，以及时长1μs的生产轨迹Trajectory_T300_Production.xtc；同时附带包含水与离子的结构文件（.gro格式）、拓扑文件（.top格式）与索引文件（.ndx格式）。 分析相关文件包括：通过Crysol计算得到的平均小角X射线散射（SAXS）曲线文件SaxsProfile.dat；用于返回时间序列的PLUMED分析文件Plumed-rerun.dat，以及存储于Colvar.dat与Fes2d-Rg_Rmsd1s2m.dat中的自由能曲面；此外还包含晶体结构与经典结构的PDB格式的CA结构文件，以及构象聚类结果文件Clustering.log。 #### 粗粒度模拟 该目录下包含四个子文件夹，分别对应带有约束核心或柔性核心的全长Dhh1模拟，以及单尾巴模拟。主目录下包含：用于计算小角X射线散射（SAXS）曲线的plumed.dat文件、.csv格式的力场参数文件，以及兼容CALVADOS框架的.yaml配置文件。 1. Flex文件夹：包含3组重复实验，以及核心与全长的回转半径（R_g）直方图，同时包含平均小角X射线散射（SAXS）曲线。 2. Constrained文件夹：包含44个初始结构、44条轨迹、回转半径（R_g）直方图与所得小角X射线散射（SAXS）曲线。 3. 两个单尾巴文件夹：均包含长轨迹与回转半径（R_g）直方图。 #### 建模相关 每个文件夹均提供RanCh生成无规卷曲结构所需的文件，包含生成10^4个构象的子文件夹、系综统计文件与平均曲线。 ### 软件版本要求 #### 全原子模拟所需软件：GROMACS 2021.4、Plumed 2.8.0 #### 粗粒度模拟所需软件：OpenMM 8.2.0、CALVADOS框架（https://github.com/KULL-Centre/CALVADOS/tree/main） #### 无规卷曲建模所需软件：ATSAS 4.0.0 中的Ranch工具
