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 sequence and direction dependence. In particular, we first introduce a method for determining biomolecular dynamics employing core-set Markov state models constructed using an advanced clustering technique. The method is validated on previously reported simulations. We then use the method to analyze extensive trajectories for four different RNA model duplexes. Results obtained using D. E. Shaw research and AMBER force fields are compared and discussed in detail and show a non-trivial interplay between the stability of intermediate states and the overall fraying kinetics.

The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models / Pinamonti, Giovanni; Paul, Fabian; Noé, Frank; Rodriguez, Alex; Bussi, Giovanni. - In: THE JOURNAL OF CHEMICAL PHYSICS. - ISSN 0021-9606. - 150:15(2019), pp. 1-9. [10.1063/1.5083227]

The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models

Rodriguez, Alex;Bussi, Giovanni
2019

Abstract

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 sequence and direction dependence. In particular, we first introduce a method for determining biomolecular dynamics employing core-set Markov state models constructed using an advanced clustering technique. The method is validated on previously reported simulations. We then use the method to analyze extensive trajectories for four different RNA model duplexes. Results obtained using D. E. Shaw research and AMBER force fields are compared and discussed in detail and show a non-trivial interplay between the stability of intermediate states and the overall fraying kinetics.
150
15
1
9
154123
https://arxiv.org/abs/1811.12144
Pinamonti, Giovanni; Paul, Fabian; Noé, Frank; Rodriguez, Alex; Bussi, Giovanni
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/20.500.11767/89934
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