Swollen-collapsed transition in random hetero-polymers

Trovato, Antonio; Mourik, Jort van; Maritan, Amos

doi:10.1007/s100510050527

Cited by 16 publications

(27 citation statements)

References 30 publications

(64 reference statements)

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“…Simplified models [18], based on a bimodal description of the energy of water in the shell around the hydrophobic molecule [19], predicted cold denaturation. Similar results were obtained using a lattice model of a random hydrophobic-hydrophilic heteropolymer interacting with the solvent [20]. Several models mimicking the interaction between water molecules and non-polar monomers have also been applied to the study of cold denaturation.…”

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confidence: 61%

Possible Mechanism for Cold Denaturation of Proteins at High Pressure

et al. 2003

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We study cold denaturation of proteins at high pressures. Using multicanonical Monte Carlo simulations of a model protein in a water bath, we investigate the effect of water density fluctuations on protein stability. We find that above the pressure where water freezes to the dense ice phase (≈ 2 kbar), the mechanism for cold denaturation with decreasing temperature is the loss of local low-density water structure. We find our results in agreement with data of bovine pancreatic ribonuclease A.Some proteins become thermodynamically unstable at low temperatures, a phenomenon called cold denaturation [1,2,3]. This phenomenon has been mainly observed at high pressures, ranging from approximately 200 MPa up to 700 MPa [4]. An explanation of the P − T phase diagram of a protein with cold denaturation has been proposed [5], but a microscopic understanding of the mechanisms leading to cold denaturation has yet to be developed, due in part to the complexity of proteinsolvent interactions.Existing theories of folding and unfolding of diluted proteins consider hydrophobicity as the driving force of protein stability [6,7,8,9,10]. In the case of apolar macromolecules, hydrophobicity has been identified with the assembly and segregation of the macromolecule to minimize the disruption of hydrogen bonds among water molecules [6,10,11]. Water tends to be removed from the surface of apolar molecules, forming a cage composed of highly organized water molecules around the molecule, where the disruption of hydrogen bonds is minimized [12]. The simplest hydrophobic model features an effective attraction between hydrophobic molecules [13], but does not reproduce cold denaturation. In order to obtain cold denaturation with this model, new studies [14,15] had to insert a temperature-dependent attraction derived from experimental observations at ambient pressure [16]. An explicit account of water around the hydrophobic molecules has also been considered in order to understand the cold denaturation process with temperatureindependent interactions. Theoretical attempts modeled the effective water-protein interactions with the free energy cost of excluding the solvent around the nonpolar molecule [11,17]. Numerical simulations based on these attempts have been applied to study the pressure denaturation found in proteins [9].Not until recently has cold denaturation been studied at the microscopic level. Simplified models [18], based on a bimodal description of the energy of water in the shell around the hydrophobic molecule [19], predicted cold denaturation. Similar results were obtained using a lattice model of a random hydrophobic-hydrophilic heteropolymer interacting with the solvent [20]. Several models mimicking the interaction between water molecules and non-polar monomers have also been applied to the study of cold denaturation. [21]. One possible reason for the inability of the previous models to capture both the molecular details of cold denaturation and the effect of pressure is the neglect of (i) correlations among water molecules...

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confidence: 61%

Possible Mechanism for Cold Denaturation of Proteins at High Pressure

et al. 2003

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“…Before we do this, we should point out that deviations from the annealed approximation were also found recently in a different model by Trovato et al [22].…”

Section: Annealed Approximationmentioning

confidence: 99%

Exactness of the annealed and the replica symmetric approximations for random heteropolymers

Bastolla

Grassberger

2001

Phys. Rev. E

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We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest neighbor pairs. For each pair, the interaction energy is an independent Gaussian variable with mean value B and variance ∆ 2 . For this model the annealed approximation is expected to become exact for low disorder, at sufficiently high dimension and in the thermodynamic limit. We show that corrections to the annealed approximation in the 3-d high temperature phase are small, but do not vanish in the thermodynamic limit, and are in good agreement with our replica symmetric calculations. Such corrections derive from the fact that the overlap between two typical chains is nonzero. We explain why previous authors had come to the opposite conclusion, and discuss consequences for the thermodynamics of the model. Numerical results were obtained by simulating chains of length N ≤ 1400 by means of the recent PERM algorithm, in the coil and molten globular phases, well above the freezing temperature.

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“…This expression is to be minimised with respect to the concentrations c {m σ } (of which there is only a finite number, even for N → ∞, and which play the role of order parameters), under the constraints (14,15). This procedure is in principle straightforward, however, since the number of order parameters (i.e.…”

Section: Rhm and Rcmmentioning

confidence: 98%

“…In the present paper we consider the three most commonly used interaction types: -In the random hydrophobic/hydrophilic model (RHM) [11][12][13][14] a label λ i is assigned to each monomer (with λ i > 0 for hydrophilic and λ i < 0 for hydrophobic monomers), and…”

Section: Model Definitionsmentioning

confidence: 99%

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Solvable lattice gas models of random hetero-polymers at finite density: I. Statics

Mourik

2000

The European Physical Journal E

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We introduce ∞-dimensional lattice gas versions of three common models of random heteropolymers, in which both the polymer density and the density of the polymer-solvent mixture are finite. These solvable models give valuable insight into the problems related to the (quenched) average over the randomness in statistical mechanical models of proteins, without having to deal with the hard geometrical constraints occurring in finite-dimensional models. Our exact solution, which is specific to the ∞-dimensional case, is compared to the results obtained by a saddle-point analysis and by the grand ensemble approach, both of which can also be applied to models of finite dimension. We find, somewhat surprisingly, that the saddle-point analysis can lead to qualitatively incorrect results.PACS. 61.41.+e Polymers, elastomers, and plastics -75.10.Nr Spin-glass and other random models

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Swollen-collapsed transition in random hetero-polymers

Cited by 16 publications

References 30 publications

Possible Mechanism for Cold Denaturation of Proteins at High Pressure

Possible Mechanism for Cold Denaturation of Proteins at High Pressure

Exactness of the annealed and the replica symmetric approximations for random heteropolymers

Solvable lattice gas models of random hetero-polymers at finite density: I. Statics

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