ﻻ يوجد ملخص باللغة العربية
Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be complemented with experimental data. We here propose a scheme based on the maximum entropy principle to combine simulations with bulk experiments. In the proposed scheme the noise arising from both the measurements and the forward models used to back calculate the experimental observables is explicitly taken into account. The method is tested on RNA nucleosides and is then used to construct chemically consistent corrections to the Amber RNA force field that allow a large set of experimental data on nucleosides and dinucleosides to be correctly reproduced. The transferability of these corrections is assessed against independent data on tetranucleotides and displays a previously unreported agreement with experiments. This procedure can be applied to enforce multiple experimental data on multiple systems in a self-consistent framework thus suggesting a new paradigm for force field refinement.
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields, it is becom
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracie
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of RNAs is oft
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time or spatial