Computational Dielectric Spectroscopy of Charged, Dipolar Systems

Schröder, Christian; Steinhauser, Othmar

doi:10.1002/9783527633272.ch10

Cited by 7 publications

(17 citation statements)

References 65 publications

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“…These values can be compared to average dipole moments computed from 1 ns slices of the trajectory data. Since the insulin species are charged, these ps are calculated with res pect to their center of mass, which proved to be reasonable in former computational dielectric studies [25,30], Experimental and computed p° of dimers and tetramers agree satisfactorily. The low value of the computed p° of the hexamer excludes a notable population at pH 10.5.…”

supporting

confidence: 63%

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Orientational Alignment of Amyloidogenic Proteins in Pre-Aggregated Solutions

Schröder

Steinhauser

Sasisanker³

et al. 2015

Phys. Rev. Lett.

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In the present study we combine dielectric relaxation spectroscopy with generalized Born simulations to explore the role of orientational order for protein aggregation in solutions of bovine pancreatic insulin at various pH conditions. Under aggregation-prone conditions at low pH, insulin monomers prefer antiparallel dipole alignments, which are consistent with the orientation of the monomeric subunits in the dimer structure. This alignment is also true for two dimers, suggesting that already at moderate protein concentrations the species assemble in equilibrium clusters, in which the molecules adopt preferred orientations also found for the protomers of the corresponding oligomers.

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confidence: 63%

“…The dielectric constant e{v) is a complex, dimensionless property consisting of rotational and-in the case of charged molecules-also translational contributions [25]. The low-frequency limit is usually restricted by electrode polarization as happened in the present case below v -2 MHz.…”

mentioning

confidence: 89%

Orientational Alignment of Amyloidogenic Proteins in Pre-Aggregated Solutions

Schröder

Steinhauser

Sasisanker³

et al. 2015

Phys. Rev. Lett.

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“…Including electrolyte in simulations of the dielectric response is a difficult technical problem since the dipole moment of the electrolyte gains discontinuous unphysical changes when ions cross the boundaries of the simulation box in simulation protocols involving periodic boundary conditions . Methods adopted to study the dielectric response of electrolytes include the unfolding of ionic trajectories into periodic images of the central simulation box and/or using ionic currents, instead of ionic dipole moments, to construct time-dependent response functions. , The reliability of both approaches has not been tested for the calculation of cross-correlations between the protein dipole and the dipole of the ionic electrolyte, which enters χ 0 in eq when the ionic component is added to water. We were not able to converge such correlations in our simulations involving charge-compensating electrolyte in the simulation box and for now leave the subject of the effect of ions on the cavity field susceptibility to future studies.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Protein Dielectrophoresis in Solution

Seyedi¹,

Matyushov

2018

J. Phys. Chem. B

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Proteins experience either pulling or repelling force from the gradient of an external electric field due to the effect known as dielectrophoresis (DEP). The susceptibility to the field gradient is traditionally calculated from the solution of the electrostatic boundary-value problem, which requires assigning a dielectric constant to the protein. This assignment is essential since the DEP susceptibility is proportional, in dielectric theories, to the Clausius-Mossotti factor, the sign of which is controlled by whether the protein dielectric constant is below (repelling) or above (pulling) the dielectric constant of water. The dielectric constant is not uniquely or even well-defined for a particle of molecular size and the Clausius-Mossotti factor is shown here to be inadequate for describing the dipolar response of the protein and hydration water. An alternative theory is developed from the standpoint of molecular properties of the protein solute and water solvent. The effective polarity of the protein molecule enters the theory in terms of the variance of its molecular dipole moment and its refractive index. Molecular dynamics (MD) simulations of the protein cytochrome c in solution are performed to calculate the dipolar susceptibilities entering the theory. We find that tumbling of the protein on the nanosecond time scale results in a positive DEP (pulling). The DEP susceptibility for cytochrome c acquired from MD simulations is 10-10 times higher than predicted by the Clausius-Mossotti factor. Nevertheless, this high DEP susceptibility is fully consistent with empirically confirmed Oncley's equation connecting the protein dipole to dielectric increments of protein solutions. For cytochrome c, high DEP susceptibilities calculated from MD are consistent with experimental dielectric data. We provide a general relation connecting the DEP susceptibility to the dielectric increment of solution.

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“…In simple molecular crystals this has been shown to take the form of a summation of lowfrequency harmonic normal modes, which can be approximated by Lorentzian dipoles (Burnett et al, 2013;Lipps et al, 2012). In liquids or amorphous systems that show no longrange order, and thus no low-frequency collective vibrational normal modes, rotational motions on these time scales are linked with the dielectric permittivity of the system and are often represented by a summation of Debye relaxations (Schrö der & Steinhauser, 2010;Lipps et al, 2012) or a Havriliak-Negami function (Schrö der & Steinhauser, 2010;Sun et al, 2012;Sibik et al, 2013). The translation counterpart to the dielectric permittivity is known as the dielectric conductivity and will further contribute to the observed THz dielectric response (Schrö der & Steinhauser, 2010;Lloyd-Hughes & Jeon, 2012).…”

Section: Introductionmentioning

confidence: 99%

“…In liquids or amorphous systems that show no longrange order, and thus no low-frequency collective vibrational normal modes, rotational motions on these time scales are linked with the dielectric permittivity of the system and are often represented by a summation of Debye relaxations (Schrö der & Steinhauser, 2010;Lipps et al, 2012) or a Havriliak-Negami function (Schrö der & Steinhauser, 2010;Sun et al, 2012;Sibik et al, 2013). The translation counterpart to the dielectric permittivity is known as the dielectric conductivity and will further contribute to the observed THz dielectric response (Schrö der & Steinhauser, 2010;Lloyd-Hughes & Jeon, 2012). It should also be noted that the observed THz dielectric spectrum will not simply be a summation of its component parts but in fact a complex mixture which can often only be decomposed using an effective medium theory (Vinh et al, 2011), if the dielectric response of many of its component parts are already known.…”

Section: Introductionmentioning

confidence: 99%

Probing temperature- and solvent-dependent protein dynamics using terahertz time-domain spectroscopy

et al. 2013

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The effect of temperature on the terahertz‐frequency‐range material properties of lyophilized and single‐crystal hen egg‐white lysozyme has been measured using terahertz time‐domain spectroscopy, with the results presented and discussed in the context of protein and solvent dynamical and glass transitions. Lyophilized hen egg‐white lysozyme was measured over a temperature range from 4 to 290 K, and a change in the dynamical behaviour of the sample at around 100 K was observed through a change in the terahertz absorption spectrum. Additionally, the effect of cryoprotectants on the temperature‐dependent absorption coefficient is studied, and it is demonstrated that terahertz time‐domain spectroscopy is capable of resolving the true glass transition temperature of single‐crystal hen egg‐white lysozyme at ∼150 K, which is in agreement with literature values measured using differential scanning calorimetry.

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Computational Dielectric Spectroscopy of Charged, Dipolar Systems

Cited by 7 publications

References 65 publications

Orientational Alignment of Amyloidogenic Proteins in Pre-Aggregated Solutions

Orientational Alignment of Amyloidogenic Proteins in Pre-Aggregated Solutions

Protein Dielectrophoresis in Solution

Probing temperature- and solvent-dependent protein dynamics using terahertz time-domain spectroscopy

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