Published August 26, 2025 | Version 2.0.0
Journal article Open

Characterization of flexible RNA binding by tandem RNA recognition motifs through integrative ensemble modelling

  • 1. ETH Zürich, Department of Biology
  • 2. ETH Zürich, Department of Chemistry and Applied Biosciences
  • 3. ETH Zurich, Department of Chemistry and Applied Biosciences

Description

Primary and processed experimental data, MMMx modelling and analysis scripts, and ensemble models for a study on RNA binding to the tandem RNA-recongnition motifs of Serine/arginine-rich splicing factor 1 (SRSF1). The set comprises the following data and scripts:

  • Primary DEER (EPR) data for the free protein and for complexes with RNA UCAUUGGAU as well as UGGAUUUUUCAU
  • Processed DEER data (distance distributions)
  • RigiFlex ensemble modelling scripts for the free protein and the two complexes to be run with MMMx
  • EnsembleFit (MMMx) scripts, including NMR paramagnetic relaxation enhancement (PRE) restraints
  • EnsembleAnalysis scripts (MMMx) for analyzing the incomplete disorder-to-order transitions from free SRSF1 to the two RNA complexes
  • ensemble models for the free protein and for complexes with RNA UCAUUGGAU as well as UGGAUUUUUCAU obtained with RigiFlex in MMMx
  • ensemble models for the free protein and for complexes with RNA UCAUUGGAU as well as UGGAUUUUUCAU obtained by a CYANA multistate computation followed by ensemble reweighting by MMMx 
  • ensemble models obtained with different approaches for generating the initial conformer pool and different reweighing procedures
  • superensembles obtained by jackknife resampling 

Files

SRSF1_free_AF3.zip

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Additional details

Funding

Swiss National Science Foundation
New types of information from pulsed electron paramagnetic resonance spectroscopy 200020_188467
Swiss National Science Foundation
Role of Disordered Regions in RNA-Binding Proteins for Function and Pathology CRSII5_170976

Software

Repository URL
https://github.com/gjeschke/MMMx
Programming language
MATLAB
Development Status
Active