Contribution of Water to Pressure and Cold Denaturation of Proteins

Abstract

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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