Internal Normal Mode Analysis applied to RNA flexibility and conformational changes

<p>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&nbsp;: 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.</p> <p><strong>In each folder</strong></p> <p><em>modes.dat</em>: results obtained by iNMA (frequency and normal modes)</p> <p><em>das1.dat</em>: conversion from internal to cartesian normal modes</p> <p>Each file <em>name_enm.pdb</em> refers to a PDB structure with a CG representation (RNA three-bead model).</p> <p><strong>Dataset 1</strong>: d1.zip</p> <p>For the first dataset, we provide MD simulations converted into CG representation (RNA three-bead model), PCA analysis,&nbsp;the results obtained by iNMA for different values of&nbsp;distance cut-off <em>R</em>_{<em>c</em>&nbsp;}&nbsp;and some scripts.</p> <p>Matlab and python&nbsp;scripts:&nbsp;</p> <p><em>analysis_pca.py</em>: to extract the different principal components</p> <p><em>analysis_PCA.m</em>: to compute overlap and cumative overlap in each folder</p> <p><em>analysis_complete_new.m</em>: to summarize the results</p> <p><strong>Dataset 2</strong>: d2.zip</p> <p>For this&nbsp;dataset, we provide the structure ensemble for&nbsp;Rfam family and the results obtained by iNMA for different values of&nbsp;distance cut-off <em>R</em>_{<em>c</em>&nbsp;}and some scripts.</p> <p>PDB files:</p> <p><em>allensemble.pdb</em>: ensemble of PDB structures for a given Rfam family</p> <p><em>allensemble_enm.pdb</em>: ensemble of PDB structures for a given Rfam family converted to&nbsp;CG representation&nbsp;(RNA three-bead model)</p> <p><em>allensemble_enm_new.pdb</em>:&nbsp;ensemble of PDB structures for a given Rfam family with the same number of&nbsp;atoms for each model&nbsp;converted to&nbsp;CG representation&nbsp;(RNA three-bead model)</p> <p><em>model.pdb</em>: reference PDB structure</p> <p><em>model_enm.pdb</em>:&nbsp;reference PDB structure converted to CG representation&nbsp;(RNA three-bead model)</p> <p>Matlab&nbsp;script:&nbsp;</p> <p><em>pca_xray_anal.m</em>: PCA analysis, overlap, cumulative overlap,&nbsp;rmsip and plots</p> <p><strong>Dataset 3</strong>: d3.zip</p> <p>PDB structure:</p> <p><em>bound.pdb</em>: bound structure</p> <p><em>unbound.pdb</em>: unbound structure</p> <p><em>diff.dat</em>: difference between bound and unbound structure after superimposition&nbsp;</p> <p>RMSD<em>n </em>with n a number:&nbsp;the first column represents&nbsp;<span class="math-tex">\(\sqrt{\beta/2}\)</span></p> <p>Matlab&nbsp;script:</p> <p><em>rmsd_anal.m</em>: analysis best mode based on RMSD</p> <p><strong>Application to the CrPV-IRES</strong>: IRES.zip</p> <p>PDB structures:</p> <p>&nbsp;<em>IRES_cg.pdb</em>: Coarse-grain structure based on the&nbsp;PDB ID&nbsp;5IT9</p> <p><em>b_end001_01_70.pdb</em>,&nbsp;<em>b_end001_01_80.pdb,&nbsp;b_end001_01_90.pdb</em>: Example of modified&nbsp;structures using the first lowest modes and different amplitudes&nbsp;<span class="math-tex">\(\beta\)</span></p> <p><em>b_end002_03_50.pdb</em>,&nbsp;<em>b_end002_03_60.pdb,&nbsp;b_end002_03_70.pdb</em>: Example of modified&nbsp;structures using the third lowest modes and different amplitudes&nbsp;<span class="math-tex">\(\beta\)</span></p>