How accurate are accurate force-fields for B-DNA
Comparison of MD structures simulated using popular force-fields (colored) with the NMR average structure (top left; greyish) of the Drew-Dickerson dodecamer. The MD structures illustrated are average conformations taken from last 20 ns of the trajectory.
Dans PD, Ivani I, Hospital A, Portella G, Gonzalez C, Orozco M.
Nucleic Acids Res 2017 Apr.; 45: 4217.
Last generation of force-fields are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as to the belief that theoretical models can substitute experimental ones in several cases. However these claims are based on limited benchmarks, where MD simulations have shown the ability to reproduce already existing ‘experimental models’, which in turn, have an unclear accuracy to represent DNA conformation in solution. In this work we explore the ability of different force-fields to predict the structure of two new B-DNA dodecamers, determined herein by means of 1H nuclear magnetic resonance (NMR). The study allowed us to check directly for experimental NMR observables on duplexes previously not solved, and also to assess the reliability of ‘experimental structures’. We observed that technical details in the annealing procedures can induce non-negligible local changes in the final structures. We also found that while not all theoretical simulations are equally reliable, those obtained using last generation of AMBER force-fields (BSC1 and BSC0OL15) show predictive power in the multi-microsecond timescale and can be safely used to reproduce global structure of DNA duplexes and fine sequence-dependent details.
PubMed: 28088759. Doi: 10.1093/nar/gkw1355. free PMC article
