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Molecular dynamics simulations of chemically modified ribonucleotides
Valerio Piomponi, Mattia Bernetti, Giovanni Bussi
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions.…
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
Nicola Calonaci, Mattia Bernetti, Alisha Jones +2
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that bind…
Integrating experimental data with molecular simulations to investigate RNA structural dynamics
Mattia Bernetti, Giovanni Bussi
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scatter…
Molecular simulations matching denaturation experiments for N6-Methyladenosine
Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti +1
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field based classical molecular dynamics simulations are a fundamen…
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Mattia Bernetti, Kathleen B. Hall, Giovanni Bussi
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural…