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） 本仓库包含用于复现bioRxiv预印本《DEAD-box蛋白Dhh1的异质溶液集合揭示模块化架构》（DOI: 10.64898/2025.12.08.692948）中展示结果的全部实验数据。 ### 压缩包内容 该压缩包包含两个核心文件夹，分别对应全原子模拟（atomistic simulations）与使用CALVADOS框架的粗粒度模拟（Coarse Grained simulations），两个文件夹中均包含基于RanCh建模（RanCh modelling）得到的分析结果。 #### 全原子模拟部分 全原子模拟文件包含：时长1.3微秒的轨迹文件Trajectory.T300.xtc、时长1微秒的生产轨迹Trajectory_T300_Production.xtc；同时附带包含溶剂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）。分析结果包括：通过Crysol计算得到的平均小角X射线散射（SAXS）轮廓文件SaxsProfile.dat；用于返回时间序列与自由能面的PLUMED分析文件Plumed-rerun.dat，其中Colvar.dat与Fes2d-Rg_Rmsd1s2m.dat包含自由能面数据，同时附带晶体结构与经典结构的PDB格式CA结构文件；以及构象聚类分析结果Clustering.log。 #### 粗粒度模拟部分 粗粒度模拟包含四个子文件夹，分别对应带有约束核心或柔性核心的全长Dhh1模拟，以及单尾域模拟。主文件夹中包含用于计算SAXS轮廓的plumed.dat文件、.csv格式的力场参数文件，以及适配CALVADOS框架的.yaml配置文件。 - Flex文件夹：包含3组重复实验数据，以及核心区域与全长Dhh1的回转半径（Rg）直方图，还有平均SAXS轮廓。 - Constrained文件夹：包含44个初始结构、44条模拟轨迹、回转半径直方图与最终得到的SAXS轮廓。 - 两个尾域子文件夹：包含长时长模拟轨迹与回转半径直方图。 #### 建模部分 每个子文件夹均提供RanCh建模生成无规卷曲结构所需的全部文件，包含存放10⁴个生成构象的文件夹、集合统计文件与平均轮廓文件。 ### 软件版本要求 #### 全原子模拟 GROMACS 2021.4、PLUMED 2.8.0 #### 粗粒度模拟 OpenMM 8.2.0、CALVADOS框架（https://github.com/KULL-Centre/CALVADOS/tree/main） #### 无规卷曲建模 ATSAS 4.0.0中的Ranch
