Critical behavior of a water monolayer under hydrophobic confinement

Bianco, Valentino; Franzese, Giancarlo

doi:10.1038/srep04440

Cited by 51 publications

(87 citation statements)

References 66 publications

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“…The residues interact through a nearest-neighbour potential given by the Miyazawa Jernigan interaction matrix. [42][43][44][45] The protein is embedded in water, explicitly modelled via the Franzese-Stanley water model which expressly accounts for many-body interactions and has been proven to reproduce, at least qualitatively, the thermodynamic and dynamic behaviour of water, [46][47][48][49][50] including its interplay with proteins. [34,35,40,[51][52][53] The coarse-grain representation of the water molecules, adopted to describe water at a constant number of molecules N, constant temperature T and constant pressure P, replaces the coordinates and orientations of the water molecules by a continuous density field and discrete bonding variables, respectively.…”

Section: The Methodsmentioning

confidence: 99%

“…(I) The water moves consist of (1) forming or breaking the hydrogen bonds and (2) rescaling the total volume of the simulation box. [50] (II) The protein moves depend on if we are performing (A) design or (B) folding: (A) Design consists in (1) point mutations of the proteins, (2) residue identity swapping, and (3), after every mutation, several water moves to equilibrate the system. [34] (B) The folding moves are (1) pivot moves, (2) corner flips and (3) crankshaft moves same as used in [43] but in 2D.…”

Section: The Methodsmentioning

confidence: 99%

“…Therefore such an index is removed from the following expression for the sake of simplicity (for general formulation see for example Ref. [34,40,[46][47][48][49][50][51][52][53][77][78][79]).…”

Section: The Modelmentioning

confidence: 99%

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In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation

2020

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We present a computational study on the folding and aggregation of proteins in an aqueous environment, as a function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding of the native conformation without the occurrence of aggregates. A further increment of the protein concentration results in the complete loss of the folded structures and induces the formation of protein aggregates. We discuss the effect of the protein interface on the water fluctuations in the protein hydration shell and their relevance in the protein‐protein interaction.

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Section: The Methodsmentioning

confidence: 99%

Section: The Methodsmentioning

confidence: 99%

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In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation

2020

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“…[34][35][36][37] Many more computer simulations investigating the phenomenology of the liquid-liquid critical point (LLCP) have been performed since then. [38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55] Detailed studies using ST2-RF have been made by Poole et al 56 using molecular dynamics, while Liu et al 57,58 simulated ST2 with Ewald summation (ST2-Ew) for the electrostatic long-range potential using Monte Carlo. Also in other water models the LLPT and its LLCP are believed to be found, for example, by Yamada et al 59 in the TIP5P model, by Paschek et al 60 in the TIP4P-Ew model, and in TIP4P/2005 by Abascal and Vega.…”

Section: Introductionmentioning

confidence: 99%

Finite-size scaling investigation of the liquid-liquid critical point in ST2 water and its stability with respect to crystallization

Kesselring

Lascaris

Franzese

et al. 2013

The Journal of Chemical Physics

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The liquid-liquid critical point scenario of water hypothesizes the existence of two metastable liquid phases-low-density liquid (LDL) and high-density liquid (HDL)-deep within the supercooled region. The hypothesis originates from computer simulations of the ST2 water model, but the stability of the LDL phase with respect to the crystal is still being debated. We simulate supercooled ST2 water at constant pressure, constant temperature, and constant number of molecules N for N ≤ 729 and times up to 1 μs. We observe clear differences between the two liquids, both structural and dynamical. Using several methods, including finite-size scaling, we confirm the presence of a liquid-liquid phase transition ending in a critical point. We find that the LDL is stable with respect to the crystal in 98% of our runs (we perform 372 runs for LDL or LDL-like states), and in 100% of our runs for the two largest system sizes (N = 512 and 729, for which we perform 136 runs for LDL or LDL-like states). In all these runs, tiny crystallites grow and then melt within 1 μs. Only for N ≤ 343 we observe six events (over 236 runs for LDL or LDL-like states) of spontaneous crystallization after crystallites reach an estimated critical size of about 70 ± 10 molecules. © 2013 AIP Publishing LLC. [http://dx

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“…Cold and P unfolding can be thermodynamically justified assuming an enthalpic gain of the solvent upon the denaturation process, without specifying the origin of this gain from molecular interactions [40]. Here, we propose a molecular-interactions model for proteins solvated by explicit water, based on the "many-body" water model [32,[41][42][43][44][45]. We demonstrate how the cold-and P-denaturation mechanisms can emerge as a competition between different free energy contributions coming from water, one from hydration water and another from bulk water.…”

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confidence: 99%

Contribution of Water to Pressure and Cold Denaturation of Proteins

2015

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The mechanisms of cold and pressure denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here, we study several cases of proteins, with or without a unique native state, with or without hydrophilic residues, by means of a coarse-grain protein model in explicit solvent. We show, using Monte Carlo simulations, that taking into account how water at the protein interface changes its hydrogen bond properties and its density fluctuations is enough to predict protein stability regions with elliptic shapes in the temperature-pressure plane, consistent with previous theories. Our results clearly identify the different mechanisms with which water participates to denaturation and open the perspective to develop advanced computational design tools for protein engineering. DOI: 10.1103/PhysRevLett.115.108101 PACS numbers: 87.15.Cc, 87.15.A-, 87.15.kr Water plays an essential role in driving the folding of a protein and in stabilizing the tertiary protein structure in its native state [1,2]. Proteins can denaturate-unfolding their structure and losing their activity-as a consequence of changes in the environmental conditions. Experimental data show that for many proteins the native folded state is stable in a limited range of temperatures T and pressures P [3][4][5][6][7][8] and that partial folding is T modulated also in "intrinsically disordered proteins" [9]. By hypothesizing that proteins have only two different states, folded (f) and unfolded (u), and that the f⟷u process is reversible at any moment, Hawley proposed a theory [10] that predicts a close stability region (SR) with an elliptic shape in the T-P plane, consistent with the experimental data [11].Cold and P denaturation of proteins have been related to the equilibrium properties of the hydration water [12][13][14][15][16][17][18][19][20][21][22][23]. However, the interpretations of the mechanism are still controversial [8,[24][25][26][27][28][29][30][31][32][33][34][35][36][37]. High-T denaturation is easily understood in terms of thermal fluctuations that disrupt the compact protein conformation: the open protein structure increases the entropy S minimizing the global Gibbs free energy G ≡ H − TS, where H is the total enthalpy. High-P unfolding can be explained by the loss of internal cavities in the folded states of proteins [36], while denaturation at negative P has been experimentally observed [38] and simulated [38,39] recently. Cold and P unfolding can be thermodynamically justified assuming an enthalpic gain of the solvent upon the denaturation process, without specifying the origin of this gain from molecular interactions [40]. Here, we propose a molecular-interactions model for proteins solvated by explicit water, based on the "many-body" water model [32,[41][42][43][44][45]. We demonstrate how the cold-and P-denaturation mechanisms can emerge as a competition between different free energy contributions coming from water, one from hydration water and another from bulk water. Moreover, we sh...

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Critical behavior of a water monolayer under hydrophobic confinement

Cited by 51 publications

References 66 publications

In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation

In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation

Finite-size scaling investigation of the liquid-liquid critical point in ST2 water and its stability with respect to crystallization

Contribution of Water to Pressure and Cold Denaturation of Proteins

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