A short guide for molecular dynamics simulations of RNA systems

Hashem, Yaser; Auffinger, Pascal

doi:10.1016/j.ymeth.2008.09.020

Cited by 71 publications

(66 citation statements)

References 163 publications

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“…30,31 Computational studies of DNA and RNA have also been elaborated in the recent book by Sponer and Lankas. 32 In relation to molecular dynamics simulations of RNA specifically, progress made in the last twenty years in this area has been summarized by McDowell et al 33 and by Hashem et al, 34 providing summaries of simulations, force field approximations, RNA interactions with solvents and ions, catalytic RNAs and RNA-protein (or small molecule) complexes. tRNA was the first RNA molecule with an X-ray structure to be studied by MD simulations.…”

Section: Introductionmentioning

confidence: 99%

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

et al. 2009

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We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water., Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA -namely major groove width, inclination and the number of base pairs in a helical twist -over a 30ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

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Section: Introductionmentioning

confidence: 99%

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

et al. 2009

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“…However, the force field description of di-and multivalent cations is much more demanding than that of monovalent ions [257]. In addition, at present, simulations are limited to below μs time scales, which is too short to observe, e.g., the dehydration of Mg 2+ [258]. What is possible in terms of kinetics, however, is the evaluation of the residence times of the more easily dehydrated K + and Na + with nucleic acid surfaces that happen on the ps to ns time scale [259][260][261][262] and for longer-lived bound metal species the estimation of lower boundaries of residence times [263].…”

Section: Further Methodsmentioning

confidence: 99%

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Pechlaner

Sigel

2011

Metal Ions in Life Sciences

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Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

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“…Here, the basic concepts in MD will be described with salient examples as relevant. Further interest is deferred to an extensive array of available reviews (Auffinger & Hashem, 2007;Ditzler et al, 2010;Egli, 2002;Hashem & Auffinger, 2009;Koehl, 2006;MacKerell & Nilsson, 2008). MD relies on empirical parameterizations to generate a potential field and then evaluates all atom-atom interactions between the macromolecule and the surrounding water and ions.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

“…From the new configuration, a new total energy (or free energy, depending on the conditions used) is calculated, and the forces and velocities are calculated again. Everything is dependent on the potential field and continual research strives to improve force field "accuracy" as judged by comparison of MD simulation results to structures predicted by ab initio studies or observed experimentally (Cheatham & Kollman, 2000;Hashem & Auffinger, 2009). Often, this has been done by adjustment of the parameters used in the analytical potential field equation of choice.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%