RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
How to understand atomistic molecular dynamics simulations of RNA and protein–RNA complexes?
We provide a critical assessment of explicit‐solvent atomistic molecular dynamics (MD)
simulations of RNA and protein/RNA complexes, written primarily for non‐specialists with an …
simulations of RNA and protein/RNA complexes, written primarily for non‐specialists with an …
Improving the performance of the amber RNA force field by tuning the hydrogen-bonding interactions
Molecular dynamics (MD) simulations became a leading tool for investigation of structural
dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force …
dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force …
Mechanistic insights into the ligand-induced unfolding of an RNA G-quadruplex
S Haldar, Y Zhang, Y **a, B Islam, S Liu… - Journal of the …, 2022 - ACS Publications
The cationic porphyrin TMPyP4 is a well-established DNA G-quadruplex (G4) binding ligand
that can stabilize different topologies via multiple binding modes. However, TMPyP4 can …
that can stabilize different topologies via multiple binding modes. However, TMPyP4 can …
Toward convergence in folding simulations of RNA tetraloops: Comparison of enhanced sampling techniques and effects of force field modifications
Atomistic molecular dynamics simulations represent an established technique for
investigation of RNA structural dynamics. Despite continuous development, contemporary …
investigation of RNA structural dynamics. Despite continuous development, contemporary …
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field
Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is
an important class of protein–RNA interactions. Many such complexes were characterized …
an important class of protein–RNA interactions. Many such complexes were characterized …
Germline AGO2 mutations impair RNA interference and human neurological development
D Lessel, DM Zeitler, MRF Reijnders… - Nature …, 2020 - nature.com
ARGONAUTE-2 and associated miRNAs form the RNA-induced silencing complex (RISC),
which targets mRNAs for translational silencing and degradation as part of the RNA …
which targets mRNAs for translational silencing and degradation as part of the RNA …
Computer folding of RNA tetraloops: identification of key force field deficiencies
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult
challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs …
challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs …
Free energy landscape of GAGA and UUCG RNA tetraloops
S Bottaro, P Banáš, J Sponer… - The journal of physical …, 2016 - ACS Publications
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using
atomistic molecular dynamics simulations. We obtain a previously unreported estimation of …
atomistic molecular dynamics simulations. We obtain a previously unreported estimation of …
UUCG RNA tetraloop as a formidable force-field challenge for MD simulations
Explicit solvent atomistic molecular dynamics (MD) simulations represent an established
technique to study structural dynamics of RNA molecules and an important complement for …
technique to study structural dynamics of RNA molecules and an important complement for …