Dielectric saturation of water in a membrane protein channel

Aguilella‐Arzo, Marcel; Andrio, Andreu; Aguilella, Vicente M.; Alcaraz, Antonio

doi:10.1039/b812775a

Cited by 62 publications

(74 citation statements)

References 48 publications

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“…We could not find any decisive literature for determining ɛ low . However, the relative permittivity of water around proteins is often assumed to be quite low for computer chemistry field or so [36]. It is possible to state one strong reason for that assumption: It is widely believed that water molecules surrounding protein form an ice-like structure and relative permittivity of ice is around 5 [37,38].…”

Section: Results and Theoretical Analysismentioning

confidence: 99%

Membrane Potential Generated by Ion Adsorption

Tamagawa

Morita

2014

Membranes

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It has been widely acknowledged that the Goldman-Hodgkin-Katz (GHK) equation fully explains membrane potential behavior. The fundamental facet of the GHK equation lies in its consideration of permeability of membrane to ions, when the membrane serves as a separator for separating two electrolytic solutions. The GHK equation describes that: variation of membrane permeability to ion in accordance with ion species results in the variation of the membrane potential. However, nonzero potential was observed even across the impermeable membrane (or separator) separating two electrolytic solutions. It gave rise to a question concerning the validity of the GHK equation for explaining the membrane potential generation. In this work, an alternative theory was proposed. It is the adsorption theory. The adsorption theory attributes the membrane potential generation to the ion adsorption onto the membrane (or separator) surface not to the ion passage through the membrane (or separator). The computationally obtained potential behavior based on the adsorption theory was in good agreement with the experimentally observed potential whether the membrane (or separator) was permeable to ions or not. It was strongly speculated that the membrane potential origin could lie primarily in the ion adsorption on the membrane (or separator) rather than the membrane permeability to ions. It might be necessary to reconsider the origin of membrane potential which has been so far believed explicable by the GHK equation.

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Section: Results and Theoretical Analysismentioning

confidence: 99%

Membrane Potential Generated by Ion Adsorption

Tamagawa

Morita

2014

Membranes

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“…is the parameter that defines a critical electric field E s ≡ 1/γ for which the dielectric saturation sets in, with α being the effective dipole moment of water molecules, for which we adopt the value α ≈ 2 D, cited in literature [37,[39][40][41][42][43][44]. We note that, when the local electric field in the electrolyte is much smaller than E s ≈ 0.1 V/nm, Eq.…”

Section: Theorymentioning

confidence: 99%

“…(1) we assume that the dielectric constant of solvent in region 3 is a function of the magnitude of the electric field, which may be modeled by the Booth model as [37,[40][41][42][43][44] 3…”

Section: Theorymentioning

confidence: 99%

“…Despite recent efforts to derive a dielectric continuum model that will take the dielectric saturation of the solvent and the effects of finite ion sizes on equal footing [36,37], it appears that old models, such as Grahame's phenomenological formula [26,38] and the Booth model [39], may provide a satisfactory description for the dielectric saturation of water and other polar solvents [40][41][42][43]. In particular, the Booth model was found to fit the results of molecular dynamics simulations of the dielectric constant of water at high electric fields [44], and was recently used to discuss the dielectric saturation of water in a membrane protein channel [40]. Moreover, the Booth model was recently combined with the BF model for steric effects to discuss the hydration repulsion between charged surfaces [41] and to conduct accurate simulations of the EDL capacitance of mesoporous electrodes [42] and ultramicroelectrodes [43].…”

Section: Introductionmentioning

confidence: 98%

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Capacitance of graphene in aqueous electrolytes: The effects of dielectric saturation of water and finite size of ions

Sharma

Mišković

2014

Phys. Rev. B

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We present a theoretical model for electrolytically top-gated graphene, in which we analyze the effects of dielectric saturation of water due to possibly strong electric fields near the surface of a highly charged graphene, as well as the steric effects due to the finite size of salt ions in an aqueous electrolyte. By combining two well-established analytical models for those two effects, we show that the total capacitance of the solution-gated graphene is dominated by its quantum capacitance for gating potentials 1 V, which is the range of primary interest for most sensor applications of graphene. On the other hand, at the potentials 1 V the total capacitance is dominated by a universal capacitance of the electric double layer in the electrolyte, which exhibits a dramatic decrease of capacitance with increasing gating potential due to the interplay of a fully saturated dielectric constant of water and ion crowding near graphene.

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“…Temperature dependence of van der Waals (vdW) forces may induce slope corrections in the same direction, whereas in the case of hydrogen bonding the slope of the temperature dependence is expected to increase (arrows around the dash-dotted line). different from that of bulk water (26), including its dependence on temperature. Third, as the binding reaction takes place within the strong confinement of the channel-forming protein, protein dielectric properties and its conformational dynamics are of importance.…”

Section: Discussionmentioning

confidence: 99%

Kinetics and thermodynamics of binding reactions as exemplified by anthrax toxin channel blockage with a cationic cyclodextrin derivative

Nestorovich

Karginov

Berezhkovskii

et al. 2012

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

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The thermodynamics of binding reactions is usually studied in the framework of the linear van't Hoff analysis of the temperature dependence of the equilibrium constant. The logarithm of the equilibrium constant is plotted versus inverse temperature to discriminate between two terms: an enthalpic contribution that is linear in the inverse temperature, and a temperature-independent entropic contribution. When we apply this approach to a particular case-blockage of the anthrax PA 63 channel by a multicharged cyclodextrin derivative-we obtain a nearly linear behavior with a slope that is characterized by enthalpy of about 1 kcal/mol. In contrast, from blocker partitioning between the channel and the bulk, we estimate the depth of the potential well for the blocker in the channel to be at least 8 kcal/mol. To understand this apparent discrepancy, we use a simple model of particle interaction with the channel and show that this significant difference between the two estimates is due to the temperature dependence of the physical forces between the blocker and the channel. In particular, we demonstrate that if the major component of blocker-channel interaction is van der Waals interactions and/or Coulomb forces in water, the van't Hoff enthalpy of the binding reaction may be close to zero or even negative, including cases of relatively strong binding. The results are quite general and, therefore, of importance for studies of enzymatic reactions, rational drug design, small-molecule binding to proteins, protein-protein interactions, and protein folding, among others.protein-ligand binding | molecular docking M otivated by the search for efficient small-molecule blockers of "virulent" transmembrane channels (1-3), we investigated the temperature behavior of the blockage reaction. The temperature dependence of the equilibrium constant of blocker association with the pore, that is, the reaction blocker(bulk) + channel(empty) ⇄ channel − blocker, was found to be surprisingly weak, with the temperature coefficient jQ 10 j ' 1.08. Applying the standard linear van't Hoff analysis to evaluate the enthalpy of an association reaction (4) to that of channel blockage (5), we arrive at an estimated enthalpy for the channel-blocker interaction of about 1 kcal/mol. However, examination of blocker partitioning between the bulk and the channel interior gives an estimate for the depth of the potential well for the blocker in the pore of at least 8 kcal/mol. Although these two estimates generally do not have to coincide, this impressive difference compelled us to take a detailed look at the assumptions that are often used in the thermodynamic analysis of blocking reactions as well as at the possible physical forces involved in the channel-blocker interaction. Our analysis is based on consideration of a simple model of particle interaction with the channel (6-8), which allows an explicit calculation of the involved thermodynamics. As might be expected, in the case of the temperatureindependent flat potential well, the enthalpy of the bindin...

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Dielectric saturation of water in a membrane protein channel

Cited by 62 publications

References 48 publications

Membrane Potential Generated by Ion Adsorption

Membrane Potential Generated by Ion Adsorption

Capacitance of graphene in aqueous electrolytes: The effects of dielectric saturation of water and finite size of ions

Kinetics and thermodynamics of binding reactions as exemplified by anthrax toxin channel blockage with a cationic cyclodextrin derivative

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