Computational Exploration of Mobile Ion Distributions around RNA Duplex

Kırmızıaltın, Serdal; Elber, Ron

doi:10.1021/jp911992t

Cited by 63 publications

(100 citation statements)

References 73 publications

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“…41,42,44,97 Our results provide experimental support for this phenomenon and highlight the importance of developing more complex atomic-level (and possibly quantum) theories to account for cation–anion correlations within the nucleic acid atmosphere. These results also provide new experimental constraints to develop and test computational models for the ion atmosphere and its properties and effects.…”

Section: Summary and Implicationssupporting

confidence: 58%

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

et al. 2015

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The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that “count” the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation–anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation–anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4–P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new results leads to a reevaluation of the strengths and limitations of Poisson–Boltzmann theory and highlights the need for next-generation atomic-level models of the ion atmosphere.

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Section: Summary and Implicationssupporting

confidence: 58%

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

et al. 2015

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“…We further evaluate the sampling using ergodic measures we have employed in the past 28–29 . In Figure 1 we illustrate that the mean force appeared to be sampled from a normal distribution after about 30 nanoseconds, suggesting uniform sampling and lack of drift.…”

Section: Methodsmentioning

confidence: 99%

Membrane Permeation of a Peptide: It Is Better to be Positive

et al. 2015

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A joint experimental and computational study investigates the translocation of a tryptophan molecule through a phospholipid membrane. Time dependent spectroscopy of the tryptophan side chain determines the rate of permeation into 150 nm phospholipid vesicles. Atomically detailed simulations are conducted to calculate the free energy profiles and the permeation coefficient. Different charging conditions of the peptide (positive, negative, or zwitterion) are considered. Both experiment and simulation reproduce the qualitative trend and suggest that the fastest permeation is when the tryptophan is positively charged. The permeation mechanism, which is revealed by Molecular Dynamics simulations, is of a translocation assisted by a local defect. The influence of long-range electrostatic interactions, such as the membrane dipole potential on the permeation process, is not significant.

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“…Computer simulations can treat discrete ions and the ion correlation and fluctuation effects (Chen et al 2009Kirmizialtin and Elber 2010;Hayes et al 2012Hayes et al , 2015Yoo and Aksimentiev 2012;Fried et al 2013;Mak and Henke 2013;Giambasu et al 2014Giambasu et al , 2015Henke and Mak 2014;Denesyuk and Thirumalai 2015;Wu et al 2015). However, a sampling of a large number of ions often demands exceedingly long computer time (Dong et al 2008).…”

Section: Introductionmentioning

confidence: 99%

MCTBI: a web server for predicting metal ion effects in RNA structures

Sun

Zhang

Chen

2017

RNA

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Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna. physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theoryexperiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures.

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Computational Exploration of Mobile Ion Distributions around RNA Duplex

Cited by 63 publications

References 73 publications

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

Cation–Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting

Membrane Permeation of a Peptide: It Is Better to be Positive

MCTBI: a web server for predicting metal ion effects in RNA structures

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