Potential of mean force between hydrophobic solutes in the Jagla model of water and implications for cold denaturation of proteins

Maiti, Moumita; Weiner, Saul; Buldyrev, Sergey V.; Stanley, H. Eugene; Sastry, Srikanth

doi:10.1063/1.3677187

Cited by 16 publications

(14 citation statements)

References 47 publications

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“…This behavior is analogous to the behavior of homopolymer47. It has been shown that at pressure P close to 0.0, the solubility of hard spheres in the Jagla solvent increases and the solvent-separated configuration of two hard spheres becomes the most stable configuration as T is decreased below 0.75 4648. It is also consistent with peaked distribution of the angle between the two subsequent bonds of a swollen homopolymer, with a maximum near 60 degrees47.…”

Section: Resultssupporting

confidence: 72%

“…In contrast to “real” water, which has three atoms and explicit hydrogen bonding, our model represents “water” as a single sphere that interacts with all other atoms through a spatially isotropic potential called the Jagla potential. The Jagla potential has been shown previously to be quite successful in displaying water-like thermodynamic, dynamic and structural anomalies4950 as well as water-like solvation thermodynamics4648. The Jagla potential has effectively two length scales – a repulsive ramp and a hard-sphere core.…”

Section: Discussionmentioning

confidence: 99%

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A Coarse-Grained Protein Model in a Water-like Solvent

Sharma

Kumar

Buldyrev

et al. 2013

Sci Rep

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Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (“H-P”) model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the “Jagla-philic” monomers to the solvent, while maintaining a “hydrophobic” core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.

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Section: Resultssupporting

confidence: 72%

Section: Discussionmentioning

confidence: 99%

A Coarse-Grained Protein Model in a Water-like Solvent

Sharma

Kumar

Buldyrev

et al. 2013

Sci Rep

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“…1(a)], an isotropic potential with two length scales, a hard-core distance a and a soft-core distance b, plus an attractive ramp that extends to a cut-off distance c. The parameterization we use, b/a = 1.72, c/a=3 and U R /U 0 = 3.56, has been shown to possess bulk water anomalies and a liquid-liquid transition [4,23]. The Jagla model was also successful in reproducing the increase of solubility upon cooling of non-polar solutes modeled as HS of diameter a [24,25].…”

Section: Simulation Detailsmentioning

confidence: 99%

Fragile-to-strong crossover coupled to the liquid-liquid transition in hydrophobic solutions

et al. 2012

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Using discrete molecular dynamics simulations we study the relation between the thermodynamic and diffusive behaviors of a primitive model of aqueous solutions of hydrophobic solutes consisting of hard spheres in the Jagla particles solvent, close to the liquid-liquid critical point of the solvent. We find that the fragile-to-strong dynamic transition in the diffusive behavior is always coupled to the low-density/high-density liquid transition. Above the liquid-liquid critical pressure, the diffusivity crossover occurs at the Widom line, the line along which the thermodynamic response functions show maxima. Below the liquid-liquid critical pressure, the diffusivity crossover occurs when the limit of mechanical stability lines are crossed, as indicated by the hysteresis observed when going from high to low temperature and vice versa. These findings show that the strong connection between dynamics and thermodynamics found in bulk water persists in hydrophobic solutions for concentrations from low to moderate, indicating that experiments measuring the relaxation time in aqueous solutions represent a viable route for solving the open questions in the field of supercooled water.

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“…Further, the Jagla model has also been shown to exhibit waterlike solvation thermodynamics [13]. In particular, the solubility of simple hard sphere solutes in the Jagla liquid is a non-monotonic function of the temperature, and furthermore, a polymer composed of such hard spheres exhibits a solvent-induced collapsed state with a stability diagram in the pressure-temperature plane reminiscent of that of a typical globular protein in water [13][14][15]. These results confirm that orientational interactions are not necessary to produce these features of water-like solvation behavior [16][17][18] and suggest that the presence of two competing length scales is a fundamental physical feature of hydrophobic hydration.…”

Section: Introductionmentioning

confidence: 99%

Temperature and length scale dependence of solvophobic solvation in a single-site water-like liquid

Dowdle

Buldyrev

Stanley

et al. 2013

The Journal of Chemical Physics

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The temperature and length scale dependence of solvation properties of spherical hard solvophobic solutes is investigated in the Jagla liquid, a simple liquid that consists of particles interacting via a spherically symmetric potential combining a hard core repulsion and a longer ranged soft core interaction, yet exhibits water-like anomalies. The results are compared with equivalent calculations for a model of a typical atomic liquid, the Lennard-Jones potential, and with predictions for hydrophobic solvation in water using the cavity equation of state and the extended simple point charge model. We find that the Jagla liquid captures the qualitative thermodynamic behavior of hydrophobic hydration as a function of temperature for both small and large length scale solutes. In particular, for both the Jagla liquid and water, we observe temperature-dependent enthalpy and entropy of solvation for all solute sizes as well as a negative solvation entropy for sufficiently small solutes at low temperature. This feature of water-like solvation is distinct from the strictly positive and temperature independent enthalpy and entropy of cavity solvation observed in the Lennard-Jones fluid. The results suggest that, compared to a simple liquid, it is the presence of a second thermally accessible repulsive energy scale, acting to increasingly favor larger separations for decreasing temperature, that is the essential characteristic of a liquid that favors low-density, open structures, and models hydrophobic hydration, and that it is the presence of this second energy scale that leads to the similarity in the behavior of water and the Jagla liquid. In addition, the Jagla liquid dewets surfaces of large radii of curvature less readily than the Lennard-Jones liquid, reflecting a greater flexibility or elasticity in the Jagla liquid structure than that of a typical liquid, a behavior also similar to that of water's hydrogen bonding network. The implications of the temperature and length scale dependence of solvation free energies in water-like liquids are explored with a simple model for the aggregation of solvophobic solutes. We show how aggregate stability depends upon the size of the aggregate and the size of its constituent solutes, and we relate this dependence to cold-induced destabilization phenomena such as the cold-induced denaturation of proteins.

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Potential of mean force between hydrophobic solutes in the Jagla model of water and implications for cold denaturation of proteins

Cited by 16 publications

References 47 publications

A Coarse-Grained Protein Model in a Water-like Solvent

A Coarse-Grained Protein Model in a Water-like Solvent

Fragile-to-strong crossover coupled to the liquid-liquid transition in hydrophobic solutions

Temperature and length scale dependence of solvophobic solvation in a single-site water-like liquid

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