General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly

Yoshidome, Takashi

doi:10.3390/e12061632

Cited by 6 publications

(10 citation statements)

References 75 publications

(174 reference statements)

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“…From this expression, we can see that the mean site occupancy for the interacting lattice-gas model can be obtained in the same way as in the noninteracting case (9),…”

Section: Partition Function For Interacting Dna Chainsmentioning

confidence: 88%

“…For instance, in the hydrophobic effect, an unfolded protein lowers the entropy by ordering the water molecules, and so the protein prefers to be in the folded state [7,8]. In the chloroplast stroma, it has been shown that there is an entropy-driven attraction that determines chloroplast ultrastructure through spontaneous Mg 2+ -induced stacking of membranes [9]. In sickle hemoglobin, the aggregation of monomers into polymers is also entropy driven, with the internal energy and entropy in a delicate balance [10].…”

Section: Introductionmentioning

confidence: 99%

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One-Loop Fluctuation Entropy of Charge Inversion in DNA

Sievert,

Bishop,

McMullen

2019

Preprint

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Experiments have revealed correlation-driven behavior of DNA in charged solutions, including charge inversion and condensation. This paper presents calculations of a lattice-gas model of charge inversion for the adsorption of charged dimers on DNA . Each adsorption site is assumed to have either a vacancy or a positively-charged dimer attached with the dimer oriented either parallel or perpendicular to the double helix DNA chain. The entropy and charge distributions of these three species are calculated including the lowest order fluctuation corrections to mean-field theory. We find that the inclusion of the fluctuation terms has a significant effect on the entropy, primarily in the regime where the dimers are repelled from the DNA molecule and compete with the chemical potential in solution.

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“…From this expression, we can see that the mean site occupancy for the interacting lattice-gas model can be obtained in the same way as in the noninteracting case (9),…”

Section: Partition Function For Interacting Dna Chainsmentioning

confidence: 88%

Section: Introductionmentioning

confidence: 99%

One-Loop Fluctuation Entropy of Charge Inversion in DNA

Sievert,

Bishop,

McMullen

2019

Preprint

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“…The activation volume of ATP binding, þ100 Å 3 , which corresponds to the volume of three water molecules, seems feasible in this context. However, we should note that there are other determinants of the apparent activation volume, such as the water-accessible surface, thermal volume, and interaction volume (58,61). A more general explanation for the pressure sensitivity of the intermolecular association process has also been proposed on the basis of the translational entropy of water (61)(62)(63).…”

Section: Discussionmentioning

confidence: 99%

“…However, we should note that there are other determinants of the apparent activation volume, such as the water-accessible surface, thermal volume, and interaction volume (58,61). A more general explanation for the pressure sensitivity of the intermolecular association process has also been proposed on the basis of the translational entropy of water (61)(62)(63). This theory predicted well that the kinetic freeenergy barrier for molecular association in general increases with pressure (T. Yoshidome and M. Ikeguchi, Yokohama City University, Yokahama, Japan, personal communication, 2013).…”

Section: Discussionmentioning

confidence: 99%

Single-Molecule Analysis of the Rotation of F1-ATPase under High Hydrostatic Pressure

Okuno

Nishiyama

Noji

2013

Biophysical Journal

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F1-ATPase is the water-soluble part of ATP synthase and is an ATP-driven rotary molecular motor that rotates the rotary shaft against the surrounding stator ring, hydrolyzing ATP. Although the mechanochemical coupling mechanism of F1-ATPase has been well studied, the molecular details of individual reaction steps remain unclear. In this study, we conducted a single-molecule rotation assay of F1 from thermophilic bacteria under various pressures from 0.1 to 140 MPa. Even at 140 MPa, F1 actively rotated with regular 120° steps in a counterclockwise direction, showing high conformational stability and retention of native properties. Rotational torque was also not affected. However, high hydrostatic pressure induced a distinct intervening pause at the ATP-binding angles during continuous rotation. The pause was observed under both ATP-limiting and ATP-saturating conditions, suggesting that F1 has two pressure-sensitive reactions, one of which is evidently ATP binding. The rotation assay using a mutant F1(βE190D) suggested that the other pressure-sensitive reaction occurs at the same angle at which ATP binding occurs. The activation volumes were determined from the pressure dependence of the rate constants to be +100 Å(3) and +88 Å(3) for ATP binding and the other pressure-sensitive reaction, respectively. These results are discussed in relation to recent single-molecule studies of F1 and pressure-induced protein unfolding.

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“…Therefore, this unfolded state keeps a certain globular shape, but it is swollen in comparison to the native conformation. 17 According to recent discoveries, 3,6,13 an increase in the hydrostatic pressure of an aqueous protein solution produces an effective force which tends to inject the solvent molecules inside the protein internal cavities and void volumes. From that point of view, proteins with more or larger cavities tend to be more destabilized by the effect of pressure.…”

Section: Introductionmentioning

confidence: 99%

Simulating protein unfolding under pressure with a coarse-grained model

Perezzan

Rey

2012

The Journal of Chemical Physics

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We describe and test a coarse-grained molecular model for the simulation of the effects of pressure on the folding/unfolding transition of proteins. The model is a structure-based one, which takes into account the desolvation barrier for the formation of the native contacts. The pressure is taken into account in a qualitative, mean field approach, acting on the parameters describing the native stabilizing interactions. The model has been tested by simulating the thermodynamic and structural behavior of protein GB1 with a parallel tempering Monte Carlo algorithm. At low effective pressures, the model reproduces the standard two-state thermal transition between the native and denatured states. However, at large pressures a new state appears. Its structural characteristics have been analyzed, showing that it corresponds to a swollen version of the native structure. This swollen state is at equilibrium with the native state at low temperatures, but gradually transforms into the thermally denatured state as temperature is increased. Therefore, our model predicts a downhill transition between the swollen and the denatured states. The analysis of the model permits us to obtain a phase diagram for the pressure-temperature behavior of the simulated system, which is compatible with the known elliptical shape of this diagram for real proteins.

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General Framework of Pressure Effects on Structures Formed by Entropically Driven Self-Assembly

Cited by 6 publications

References 75 publications

One-Loop Fluctuation Entropy of Charge Inversion in DNA

One-Loop Fluctuation Entropy of Charge Inversion in DNA

Single-Molecule Analysis of the Rotation of F1-ATPase under High Hydrostatic Pressure

Simulating protein unfolding under pressure with a coarse-grained model

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