Internal Normal Mode Analysis applied to RNA flexibility and conformational changes

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.

In each folder

modes.dat: results obtained by iNMA (frequency and normal modes)

das1.dat: conversion from internal to cartesian normal modes

Each file name_enm.pdb refers to a PDB structure with a CG representation (RNA three-bead model).

Dataset 1: 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 R_c  and some scripts.

Matlab and python scripts: 

analysis_pca.py: to extract the different principal components

analysis_PCA.m: to compute overlap and cumative overlap in each folder

analysis_complete_new.m: to summarize the results

Dataset 2: 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 R_c  and some scripts.

PDB files:

allensemble.pdb: ensemble of PDB structures for a given Rfam family

allensemble_enm.pdb: ensemble of PDB structures for a given Rfam family converted to CG representation (RNA three-bead model)

allensemble_enm_new.pdb: 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)

model.pdb: reference PDB structure

model_enm.pdb: reference PDB structure converted to CG representation (RNA three-bead model)

Matlab script: 

pca_xray_anal.m: PCA analysis, overlap, cumulative overlap, rmsip and plots

Dataset 3: d3.zip

PDB structure:

bound.pdb: bound structure

unbound.pdb: unbound structure

diff.dat: difference between bound and unbound structure after superimposition 

RMSDn with n a number: the first column represents \(\sqrt{\beta/2}\)

Matlab script:

rmsd_anal.m: analysis best mode based on RMSD

Application to the CrPV-IRES: IRES.zip

PDB structures:

 IRES_cg.pdb: Coarse-grain structure based on the PDB ID 5IT9

b_end001_01_70.pdb, b_end001_01_80.pdb, b_end001_01_90.pdb: Example of modified structures using the first lowest modes and different amplitudes \(\beta\)

b_end002_03_50.pdb, b_end002_03_60.pdb, b_end002_03_70.pdb: Example of modified structures using the third lowest modes and different amplitudes \(\beta\)