Effects of Ion Size and Valence on Ion Distribution in Mixed Counterion Systems of a Rodlike Polyelectrolyte Solution. 2. Mixed-Valence Counterion Systems

and, Takuhiro Nishio; Minakata, Akira

doi:10.1021/jp022531a

Cited by 18 publications

(20 citation statements)

References 23 publications

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“…Although the limitations of NLPB in the treatment of ion sizes and correlations have been extensively discussed 15,17,18,34,39,52 , the actual extent of these limitations was not known and has been quantitatively revealed for the first time in this work. The observed deviations are larger for divalent than monovalent cations (Figs.…”

Section: Discussionmentioning

confidence: 90%

“…Intensive theoretical work has suggested that the accuracy of NLPB in predicting ion association is limited by the inability of this theory to account for ion correlation, in addition to the limitations in treating ion size effects discussed above 16,17 . However, there is no straightforward and quantitative experimental benchmark for comparison.…”

Section: Competitive Association Of Cations: Assessing the Effects Ofmentioning

confidence: 99%

“…Theoretical studies suggest that spatial correlations of ions stabilize high cation densities close to the nucleic acid surface, resulting in a higher total cation association than predicted by PB 11,16,34 . The correlation effects are predicted to increase with ion valence and the charge density of the polyelectrolyte 16,17,51 . Accordingly, stronger correlations and thus a larger increase of the ion occupancy relative to the NLPB prediction are expected for divalent cations over monovalent cations.…”

Section: Competitive Association Of Cations: Assessing the Effects Ofmentioning

confidence: 99%

“…This average ion density (Fig. 1C) does not take into account correlations expected because the position of one ion influences the preferred position of other ions in the atmosphere 16,17 .…”

Section: Introductionmentioning

confidence: 99%

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Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

et al. 2007

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The ion atmosphere around nucleic acids critically affects biological and physical processes such as chromosome packing, RNA folding, and molecular recognition. However, the dynamic nature of the ion atmosphere renders it difficult to characterize. The basic thermodynamic description of this atmosphere, a full accounting of the type and number of associated ions, has remained elusive. Here we provide the first complete accounting of the ion atmosphere, using buffer equilibration and atomic emission spectroscopy (BE-AES) to accurately quantitate the cation association and anion depletion. We have examined the influence of ion size and charge on ion occupancy around simple, well-defined DNA molecules. The relative affinity of monovalent and divalent cations correlates inversely with their size. Divalent cations associate preferentially over monovalent cations; e.g., with Na + in four-fold excess of Mg 2+ (20 vs. 5 mM), the ion atmosphere nevertheless has three-fold more Mg 2+ than Na + . Further, the dicationic polyamine putrescine 2+ does not compete effectively for association relative to divalent metal ions, presumably because of its lower charge density. These and other BE-AES results can be used to evaluate and guide the improvement of electrostatic treatments. As a first step, we compare the BE-AES results to predictions from the widely-used nonlinear Poisson Boltzmann (NLPB) theory and assess the applicability and precision of this theory. In the future, BE-AES in conjunction with improved theoretical models, can be applied to complex binding and folding equilibria of nucleic acids and their complexes, to parse the electrostatic contribution from the overall thermodynamics of important biological processes.

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Section: Discussionmentioning

confidence: 90%

Section: Competitive Association Of Cations: Assessing the Effects Ofmentioning

confidence: 99%

Section: Competitive Association Of Cations: Assessing the Effects Ofmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

et al. 2007

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“…The potential in the inner zone (at distance ba) follows lineally as in a homogeneous solid state body; that allows to consider the polyelectrolyte chain as a coaxial cylindrical condenser. The presence of two kinds of counterions with different radius and valence can be considered by introducing an additional cylinder in the inner zone [18,19]. The potential 1 of the cylinder with radius b is determined by the total chain's charge including the adsorbed ions.…”

Section: Cylinder Cell Modelmentioning

confidence: 99%

Electric Properties of Carboxymethyl Cellulose

Zhivkov¹

2013

Cellulose - Fundamental Aspects

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Brownian dynamics study of the association between the 70S ribosome and elongation factor G

et al. 2011

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Protein synthesis on the ribosome involves a number of external protein factors that bind at its functional sites. One key factor is the elongation factor G (EF-G) that facilitates the translocation of transfer RNAs between their binding sites, as well as advancement of the messenger RNA by one codon. The details of the EF-G/ribosome diffusional encounter and EF-G association pathway still remain unanswered. Here, we applied Brownian dynamics methodology to study bimolecular association in the bacterial EF-G/70S ribosome system. We estimated the EF-G association rate constants at 150 and 300 mM monovalent ionic strengths and obtained reasonable agreement with kinetic experiments. We have also elucidated the details of EF-G/ribosome association paths and found that positioning of the L11 protein of the large ribosomal subunit is likely crucial for EF-G entry to its binding site. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 616–627, 2011.

show abstract

Effects of Ion Size and Valence on Ion Distribution in Mixed Counterion Systems of a Rodlike Polyelectrolyte Solution. 2. Mixed-Valence Counterion Systems

Cited by 18 publications

References 23 publications

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Electric Properties of Carboxymethyl Cellulose

Brownian dynamics study of the association between the 70S ribosome and elongation factor G

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