Simulations of RNA Interactions with Monovalent Ions

Chen, Alan; Marucho, Marcelo; Baker, Nathan A.; Pappu, Rohit V.

doi:10.1016/s0076-6879(09)69020-0

Cited by 57 publications

(56 citation statements)

References 39 publications

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“…Mao et al showed that if one were to use explicit representations for solvent molecules, one would need cubic boxes ca 120 Å to a side with periodic boundary conditions for 28-residue to 30-residue highly charged IDPs in order to obtain an accurate assessment of conformational ensembles. 23 Third, for highly charged systems, the accurate modeling of the effects of neutralizing counterions and excess co-ions and counterions mandates the use of large simulation cells, as demonstrated by Chen et al 59,60 Taken together, the "medium-throughput" approach that we need to pursue-whereby we query conformational distributions of ca 100 distinct polyelectrolytic/polyampholytic sequences in the 28-30 residue range that is necessary to arrive at robust conclusions regarding the nature and degree of conformational heterogeneity within an IDP/IDR family-is difficult (if not intractable) at this stage, with explicit representations of solvent molecules.…”

Section: Justification For the Model And The Sampling Approachmentioning

confidence: 99%

N-Terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins

Das

Crick

Pappu

2012

Journal of Molecular Biology

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Section: Justification For the Model And The Sampling Approachmentioning

confidence: 99%

N-Terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins

Das

Crick

Pappu

2012

Journal of Molecular Biology

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“…27 Classical Molecular Dynamics (MD) simulations have been widely used to provide directly atomistic detailed information on the dynamics and structural ion-binding feature of RNA systems. 16,[28][29][30][31] For example, Auffinger and Westhof showed the sequence dependence of K + ion binding to nucleic acids using nanosecond atomistic simulations, 16 and recently a study by Singh et. al.…”

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confidence: 99%

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

Allnér

Nilsson

Villa

2012

J. Chem. Theory Comput.

355

417

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Magnesium ions have an important role in the structure and folding mechanism of ribonucleic systems. To properly simulate these biophysical processes, the applied molecular models should reproduce, among others, the kinetic properties of the ions in water solution. Here, we have studied the kinetics of the binding of magnesium ions with water molecules and nucleic acids systems using molecular dynamics simulation in detail. We have validated the parameters used in biomolecular force fields, such as AMBER and CHARMM, for Mg2+ ions, and also for the biological relevant ions, Na+, K+ and Ca2+ together with three different water models (TIP3P, SPC/E and TIP5P). The results show that Mg2+ ions have a slower exchange rate than Na+, K+ and Ca2+ in agreement with experimental trend, but the simulated value underestimates the experimentally observed Mg2+-water exchange rate with several orders of magnitudes, irrespective of force field and water model. A new set of parameters for Mg2+ was developed to reproduce the experimental kinetic data. This set also leads to better reproduction of structural data than existing models. We have applied the new parameters set to Mg2+ binding with a mono-phosphate model system and with the purine riboswitch, add A-riboswitch. In line with the Mg2+-water results, the newly developed parameters show a better description of the structure and kinetic of the Mg2+-phosphate 2 binding than all other models. The characterization of the ion binding to the riboswitch system shows that the new parameter set does not affect the global structure of the ribonucleic acid system or the number of ions involved in direct or indirect binding. A slight decrease in the number of water-bridged contacts between A-riboswitch and Mg2+ ion is observed. The results support the ability of the newly developed parameters to improve the kinetic description of the Mg2+ and phosphate ions and their applicability in nucleic acid simulation.

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“…NLPB is a mean field treatment, and neglects ion-ion correlations [23, 24] and ion size effects [25–27]. For monovalent ions where these correlations are weak, NLPB performs well, but is less accurate for divalent Mg 2+ [26, 28].…”

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Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

et al. 2015

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RNA is highly sensitive to the ionic environment, and typically requires Mg2+ to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg2+ ions explicitly to account for ion-ion correlations neglected by mean field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, non-limiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg2+ associated with the RNA, Γ2+, because Γ2+ is directly related to the Mg2+-RNA interaction free energy. The excellent agreement with experiment demonstrates the model captures the ionic dependence of the RNA free energy landscape.

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Simulations of RNA Interactions with Monovalent Ions

Cited by 57 publications

References 39 publications

N-Terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins

N-Terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

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