Internal Normal Mode Analysis applied to RNA flexibility and conformational changes

We investigated the capability of internal normal modes to reproduce RNA flexibility and predict observed RNA conformational changes, and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified representation of RNA structure and its potential energy. In this study, we considered three main data sets to investigate different aspects : i) one based on single-stranded RNA molecules for which all-atom MD simulations were computed; ii) one based on the available structures belonged to a specific Rfam family; iii) one based on the transition from unbound to bound RNA. A new version with the application to the CrPV-IRES is also present in the new version2 (10.5281/zenodo.7672081) Open Access. <strong>In each folder</strong> <em>modes.dat</em>: results obtained by iNMA (frequency and normal modes) <em>das1.dat</em>: conversion from internal to cartesian normal modes Each file <em>name_enm.pdb</em> refers to a PDB structure with a CG representation (RNA three-bead model). <strong>Dataset 1</strong>: d1.zip For the first dataset, we provide MD simulations converted into CG representation (RNA three-bead model), PCA analysis, the results obtained by iNMA for different values of distance cut-off <em>R</em>_<em>c</em> and some scripts. Matlab and python scripts: <em>analysis_pca.py</em>: to extract the different principal components <em>analysis_PCA.m</em>: to compute overlap and cumative overlap in each folder <em>analysis_complete_new.m</em>: to summarize the results <strong>Dataset 2</strong>: d2.zip For this dataset, we provide the structure ensemble for Rfam family and the results obtained by iNMA for different values of distance cut-off <em>R</em>_<em>c</em>and some scripts. PDB files: <em>allensemble.pdb</em>: ensemble of PDB structures for a given Rfam family <em>allensemble_enm.pdb</em>: ensemble of PDB structures for a given Rfam family converted to CG representation (RNA three-bead model) <em>allensemble_enm_new.pdb</em>: ensemble of PDB structures for a given Rfam family with the same number of atoms for each model converted to CG representation (RNA three-bead model) <em>model.pdb</em>: reference PDB structure <em>model_enm.pdb</em>: reference PDB structure converted to CG representation (RNA three-bead model) Matlab script: <em>pca_xray_anal.m</em>: PCA analysis, overlap, cumulative overlap, rmsip and plots <strong>Dataset 3</strong>: d3.zip PDB structure: <em>bound.pdb</em>: bound structure <em>unbound.pdb</em>: unbound structure <em>diff.dat</em>: difference between bound and unbound structure after superimposition RMSD<em>n </em>with n a number: the first column represents \(\sqrt{\beta/2}\) Matlab script: <em>rmsd_anal.m</em>: analysis best mode based on RMSD