23Na NMR study of the effect of organic osmolytes on DNA counterion atmosphere

Flock, S.; Labarbe, Rudi; Houssier, Claude

doi:10.1016/s0006-3495(96)79354-2

Cited by 27 publications

(23 citation statements)

References 31 publications

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“…Conceptually, counterions would “condense” onto the polyelectrolyte, effectively renormalizing its charge. Support for the main tenet of CC theory, that of a salt‐invariant counterion domain near highly charged polyelectrolytes, comes from a wealth of data on the atomic,52–56 kinetic,57–69 and colligative70–81 properties of such systems. Although experimental proof of a well‐defined region of condensed counterions is tentative,19, 54, 82 detailed molecular dynamics and Monte Carlo83–85 simulations of all‐atom DNA do show a region near the surface with fairly uniform counterion concentration.…”

Section: Introductionmentioning

confidence: 99%

Counterion condensation and shape within Poisson–Boltzmann theory

Lamm

Pack

2010

Biopolymers

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An analytical approximation to the nonlinear Poisson-Boltzmann (PB) equation is applied to charged macromolecules that possess one-dimensional symmetry and can be modeled by a plane, infinite cylinder, or sphere. A functional substitution allows the nonlinear PB equation subject to linear boundary conditions to be transformed into an approximate linear (Debye-Hückel-type) equation subject to nonlinear boundary conditions. A simple analytical result for the surface potential of such polyelectrolytes follows, leading to expressions for the amount of condensed (or renormalized) charge and the electrostatic Helmholtz energy for polyelectrolytes. Analytical high-charge/low-salt and low-charge/high-salt limits are shown to be similar to results obtained by others based on PB or counterion condensation theory. Several important general observations concerning polyelectrolytes treated within the context of PB theory can be made including: (1) all charged surfaces display some counterion condensation for finite electrolyte concentration, (2) the effect of surface geometry is described primarily by the sum of the Debye constant and the mean curvature of the surface, (3) two surfaces with the same surface charge density and mean curvature condense approximately identical fractions of counterions, (4) the amount of condensation is not determined by a predefined "condensation distance" although such a distance can be determined uniquely from it, and (5) substantial condensation occurs if the Debye constant of the electrolyte is much less than the mean curvature of a highly charged polyelectrolyte.

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Section: Introductionmentioning

confidence: 99%

Counterion condensation and shape within Poisson–Boltzmann theory

Lamm

Pack

2010

Biopolymers

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“…Coulombic forces are inversely proportional to the dielectric constant of a medium and distances between two interacting charges. THP molecules most likely increase the dielectric constant of the medium like other zwitterionic compounds (25) and, if not repelled from protein or DNA surface upon enzyme-DNA complex formation, may cause a steric interference to the decrease of distances of charges interaction. Both effects will eventually lead to a decrease in favorable energetic contributions of protein-phosphate contacts.…”

Section: Discussionmentioning

confidence: 99%

“…2 Moreover, THP(B) at certain concentrations, can, like betaine (22), eliminate base pair composition dependence of DNA melting. 2 In addition, THP molecules share similarity in structure and geometry with pyrimidine bases and have the zwitterionic character, which was recently shown to be responsible for modification of DNA electrostatic interaction with counterions by a number of osmolytes (25). These notions led us to suggest that the impact of osmoprotectants, and THPs in particular, on protein-DNA interaction is, likely, underestimated.…”

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confidence: 99%

Effect of Tetrahydropyrimidine Derivatives on Protein-Nucleic Acids Interaction

Malin¹,

Iakobashvili

Lapidot

1999

Journal of Biological Chemistry

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2-Methyl-4-carboxy,5-hydroxy-3,4,5,6-tetrahydropyrimidine (THP(A) or hydroxyectoine) and 2-methyl,4-carboxy-3,4,5,6-tetrahydropyrimidine (THP(B) or ectoine) are now recognized as ubiquitous bacterial osmoprotectants. To evaluate the impact of tetrahydropyrimidine derivatives (THPs) on protein-DNA interaction and on restriction-modification systems, we have examined their effect on the cleavage of plasmid DNA by 10 type II restriction endonucleases. THP(A) completely arrested the cleavage of plasmid and bacteriophage DNA by EcoRI endonuclease at 0.4 mM and the oligonucleotide (d(CGCGAATTCGCG)) 2 at about 4.0 mM. THP(B) was 10-fold less effective than THP(A), whereas for betaine and proline, a notable inhibition was observed only at 100 mM. Similar effects of THP(A) were observed for all tested restriction endonucleases, except for SmaI and PvuII, which were inhibited only partially at 50 mM THP(A). No effect of THP(A) on the activity of DNase I, RNase A, and Taq DNA polymerase was noticed. Gelshift assays showed that THP(A) inhibited the EcoRI-(d-(CGCGAATTCGCG)) 2 complex formation, whereas facilitated diffusion of EcoRI along the DNA was not affected. Methylation of the carboxy group significantly decreased the activity of THPs, suggesting that their zwitterionic character is essential for the inhibition effect. Possible mechanisms of inhibition, the role of THPs in the modulation of the protein-DNA interaction, and the in vivo relevance of the observed phenomena are discussed.Two tetrahydropyrimidine derivatives identified in Streptomyces bacteria (1-3), one a previously unknown metabolite, THP(A), 1 and the other previously identified (as ectoine) in halophilic bacteria (4), THP(B), are now recognized as widely spread osmoprotectants within the bacterial world (5). The role and activities of THPs are of special interest as they represent a limited group of osmoprotectants that are synthesized de novo, in the bacterial cell, in contrast to those transported from the medium (6). Their synthesis in a number of Streptomyces strains as a response to increased salinity and elevated temperature was recently described (7). THPs are small molecules, highly soluble in water and neutral at physiological pH. NMR and x-ray crystallography data show that THPs are zwitterionic molecules with a delocalized charge in the NCN group (Fig. 1) and form the half-chair conformation (8).More information has been accumulated lately on THPs activity in living cells. It was found that exogenously provided ectoine (THP(B)) could reverse growth inhibition, caused by osmotic stress, in Escherichia coli (9), Corynebacterium glutamicum (10), and the soil bacterium Rhizobium meliloti (11). We demonstrated that exogenously provided THP(A), like THP(B), reversed inhibition of E. coli growth by osmotic stress, and moreover, both THP(A) and THP(B) could stimulate growth of E. coli at an elevated temperature (43°C) (7). Recently cloned genes for ectoine synthesis from Halomonas elongata (12) and from Marinococcus halophilus (13) were demonstrated ...

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“…[44] The amino acids showed a behaviour opposite to that of the polyols: The half-height linewidth was found to decrease in the presence of the amino acids but a sharp increase was observed with the added polyols. From the analysis of the NMR data in the framework of the CC theory, the influence of the amino acids was correlated with the decrease of the population of the bound counterions, caused by the increase of the medium dielectric constant and, therefore, by the decrease [*] diMeTAP 2,7-dimethyl-1,4,5,8-tetraazaphenanthrene; phen 1,10-phenanthroline; hat 1,4,5,8,9,12-hexaazatriphenylene. of electrostatic interactions with DNA.…”

Section: The Ligand ± Dna Interactionmentioning

confidence: 95%