DOI: 10.5281/zenodo.7672081
title: Internal Normal Mode Analysis applied to RNA flexibility and conformational changes

description: We investigated the capability of internal normal modes to reproduce RNA dynamics 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 rep- resentation 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. <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><sub><em>c</em> </sub> 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><sub><em>c</em> </sub>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 <strong>Application to the CrPV-IRES</strong>: IRES.zip PDB structures: <em>IRES_cg.pdb</em>: Coarse-grain structure based on the PDB ID 5IT9 <em>b_end001_01_70.pdb</em>, <em>b_end001_01_80.pdb, b_end001_01_90.pdb</em>: Example of modified structures using the first lowest modes and different amplitudes \(\beta\) <em>b_end002_03_50.pdb</em>, <em>b_end002_03_60.pdb, b_end002_03_70.pdb</em>: Example of modified structures using the third lowest modes and different amplitudes \(\beta\)