Research data supporting: The Heterogeneous Solution Ensemble of the DEAD-box Protein Dhh1 Reveals a Modular Architecture

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 containing water and ions, a topology file , an index file . 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 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