Recent Applications of Kirkwood–Buff Theory to Biological Systems

Pierce, Veronica; Kang, Myungshim; Aburi, Mahalaxmi; Weerasinghe, Samantha; Smith, Paul E.

doi:10.1007/s12013-007-9005-0

Cited by 205 publications

(318 citation statements)

References 167 publications

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“…A consistent description for IL-water mixtures, based on thermodynamic and statistical mechanics arguments is provided by the Kirkwood-Buff (KB) theory, which was originally developed as a molecular theory of solutions and solution mixtures 47,[65][66][67][68][69][70][71][72][73][74][75][76][77][78][79][80][81] . It has to be noted that the KB theory does not imply any restrictions on the molecular structure of the water molecules and the ion species, such that the theory is applicable for all systems in the liquid state.…”

Section: Kirkwood-buff Theorymentioning

confidence: 99%

“…The corresponding number of excess particles or molecules can be calculated by N xs i j = ρ j G i j with the bulk number density ρ j and the additional requirement N xs i j = N xs ji . Although the original KB theory and the KB integrals were formulated in order to describe molecular fluctuations in the grandcanonical µV T ensemble, it was shown that identical expressions can be derived equivalently in several other ensembles and specifically in the NV T and the N pT ensemble 69,83 . We point the reader to Refs.…”

Section: Kirkwood-buff Theorymentioning

confidence: 99%

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The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches

Kobayashi

Reid

Shimizu

et al. 2017

Phys. Chem. Chem. Phys.

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We study the properties of residual water molecules at different mole fractions in dialkylimidazolium based ionic liquids (ILs), namely 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM/BF4) and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM/BF4) by means of atomistic molecular dynamics (MD) simulations. The corresponding Kirkwood-Buff (KB) integrals for the water-ion and ion-ion correlation behavior are calculated by a direct evaluation of the radial distribution functions. The outcomes are compared to the corresponding KB integrals derived by an inverse approach based on experimental data. Our results reveal a quantitative agreement between both approaches, which paves a way towards a more reliable comparison between simulation and experimental results. The simulation outcomes further highlight that water even at intermediate mole fractions has a negligible influence on the ion distribution in the solution. More detailed analysis on the local/bulk partition coefficients and the partial structure factors reveal that water molecules at low mole fractions mainly remain in the monomeric state. A non-linear increase of higher order water clusters can be found at larger water concentrations. For both ILs, a more pronounced water coordination around the cations when compared to the anions can be observed, which points out that the IL cations are mainly responsible for water pairing mechanisms. Our simulations thus provide detailed insights in the properties of dialkylimidazolium based ILs and their effects on water binding.

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Section: Kirkwood-buff Theorymentioning

confidence: 99%

Section: Kirkwood-buff Theorymentioning

confidence: 99%

The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches

Kobayashi

Reid

Shimizu

et al. 2017

Phys. Chem. Chem. Phys.

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“…1, K γ is the quotient of biopolymer activity coefficients corresponding to the concentration quotient K obs and μ 23 ¼ RTd ln γ 2 ∕dm 3 † ; μ 23 is closely related to the preferential interaction coefficient Γ μ3 (4,5), which can be predicted if the ion distributions near the biopolymer are known (26,27 …”

Section: Background On Solute M-values and Chemical Potential Derivatmentioning

confidence: 99%

Why Hofmeister effects of many salts favor protein folding but not DNA helix formation

Pegram

Wendorff²,

Erdmann³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

162

288

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The majority (∼70%) of surface buried in protein folding is hydrocarbon, whereas in DNA helix formation, the majority (∼65%) of surface buried is relatively polar nitrogen and oxygen. Our previous quantification of salt exclusion from hydrocarbon (C) accessible surface area (ASA) and accumulation at amide nitrogen (N) and oxygen (O) ASA leads to a prediction of very different Hofmeister effects on processes that bury mostly polar (N, O) surface compared to the range of effects commonly observed for processes that bury mainly nonpolar (C) surface, e.g., micelle formation and protein folding. Here we quantify the effects of salts on folding of the monomeric DNA binding domain (DBD) of lac repressor (lac DBD) and on formation of an oligomeric DNA duplex. In accord with this prediction, no salt investigated has a stabilizing Hofmeister effect on DNA helix formation. Our ASA-based analyses of model compound data and estimates of the surface area buried in protein folding and DNA helix formation allow us to predict Hofmeister effects on these processes. We observe semiquantitative to quantitative agreement between these predictions and the experimental values, obtained from a novel separation of coulombic and Hofmeister effects. Possible explanations of deviations, including salt-dependent unfolded ensembles and interactions with other types of surface, are discussed.Hofmeister salts | m-values | thermodynamics S alts typically exert both specific (Hofmeister) and nonspecific (coulombic) effects on biomolecular processes (1-6). To manipulate and probe biopolymer processes using salts, it is extremely important to develop quantitative methods to interpret and predict these effects in terms of structure. coulombic, valencespecific effects of salt ions (due to screening of surface charges) are most significant at relatively low salt concentrations (<0.1 M). At higher concentrations (>0.1 M), ion-specific effects and relatively nonspecific osmotic effects (due to the lowering of water activity) become increasingly significant. In 1888, Franz Hofmeister discovered that the effectiveness of salts for protein precipitation generally followed a specific order, regardless of the protein being investigated (7). Since then, the so-called Hofmeister series of salt effects has been observed in physical properties of aqueous salt solutions (e.g., surface tension and surface potential) (8, 9), as well as salt effects on a variety of macromolecular processes (e.g., micelle formation, "salting out" nonpolar compounds, and protein folding) (10-13). The general ranking of ions, in decreasing order of effectiveness (best to worst) in driving processes where surface area is buried (e.g., folding and precipitation) or macroscopic surface is lost (transfer of water from the air-water interface to bulk), is as follows (14):Although it is generally accepted that interactions of salts with hydrocarbon surface are unfavorable and salt-specific, following the above order (1,3,11,(14)(15)(16), less is known about the interactions of Hofmeister sa...

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“…[2][3][4] Consequently, KB theory has been used to understand a variety of solution behaviors. [2][3][4][5] The central focus of KB theory is the KB integrals ͑G ij ͒ between the different species i and j in a solution mixture,…”

Section: Introductionmentioning

confidence: 99%

On the Kirkwood–Buff inversion procedure

Smith

2008

The Journal of Chemical Physics

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A general approach is presented to express the Kirkwood-Buff integrals, the central component of the Kirkwood-Buff theory of solutions, in terms of thermodynamic properties of solution mixtures. A general expression valid for any number of components is provided in terms of matrix cofactors, while explicit expressions are given for three and four component mixtures. The corresponding symmetric ideal solution values are also presented for four and higher component mixtures.

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Recent Applications of Kirkwood–Buff Theory to Biological Systems

Cited by 205 publications

References 167 publications

The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches

The properties of residual water molecules in ionic liquids: a comparison between direct and inverse Kirkwood–Buff approaches

Why Hofmeister effects of many salts favor protein folding but not DNA helix formation

On the Kirkwood–Buff inversion procedure

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