Decomposition of Protein Experimental Compressibility into Intrinsic and Hydration Shell Contributions

Dadarlat, Voichita M.; Post, Carol Beth

doi:10.1529/biophysj.106.087726

Cited by 53 publications

(76 citation statements)

References 57 publications

(62 reference statements)

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“…[1][2][3][4][5][6][7][8][9] Many biologically important processes take place at biointerfaces. These include transport, oxidation, and reduction of molecules at cell membranes and the recognition of proteins and DNA by drugs.…”

Section: Introductionmentioning

confidence: 99%

Interplay between Hydration and Electrostatic Attraction in Ligand Binding: Direct Observation of Hydration Barrier at Reverse Micellar Interface

2007

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The recognition of a charged biomolecular surface by an oppositely charged ligand is governed by electrostatic attraction and surface hydration. In the present study, the interplay between electrostatic attraction and hydration at the interface of a negatively charged reverse micelle (RM) at different temperatures has been addressed. Temperature-dependent solvation dynamics of a probe H33258 (H258) at the reverse micellar interface explores the nature of hydration at the interface. Up to 45°C, the environmental dynamics reported by the interfacebinding probe H258 becomes progressively faster with increasing temperature and follows the Arrhenius model. Above 45°C, the observed dynamics slows down with increasing temperature, thus deviating from the Arrhenius model. The slower dynamics at higher temperatures is interpreted to be due to increasing contributions from the motions of the surfactant head groups, indicating the proximity of the probe to the interface at higher temperatures. This suggests an increased electrostatic attraction between the ligand and interface at higher temperatures and is attributed to the change in hydration. Densimetric and acoustic studies, indeed, show a drastic increase in the apparent specific adiabatic compressibility of the water molecules present in RMs after 45°C, revealing the existence of a softer hydration shell at higher temperatures. Our study indicates that the hydration layer at a charged interface acts both as physical and energetic barrier to electrostatic interactions of small ligands at the interface.

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Section: Introductionmentioning

confidence: 99%

Interplay between Hydration and Electrostatic Attraction in Ligand Binding: Direct Observation of Hydration Barrier at Reverse Micellar Interface

2007

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“…Some works suggest a decrease of interfacial water density [54][55][56][57], while recent simulations show an increase of density in the first hydration shell of any solute [58] and an increase of compressibility near Φ solutes with size ≳0.5 nm for water [29,52,59] or waterlike solvents [60] with respect to bulk. Increasing P induces a further increase of density and reduces the effect of the Φ interface on the compressibility of the hydration shell [29,52,61,62].…”

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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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“…The polar category includes atoms with an absolute partial charge |q i | > 0.3e, excluding those atoms defined as charged. All other atoms are non-polar atoms (Dadarlat and Post, 2003;Dadarlat and Post, 2006). improved equation 22 for globular proteins as γ (cm 3 mol -1 bar -1 Å -2 ) is the unit compressibility contribution of the solvent accessible surface area (Å 2 ) due to different hydrations (i.e., charged, polar and non-polar) on the protein solvent accessible surface; θ is the solvent accessible surface area (Å 2 ) of one mole of protein; M is protein molecular weight; and the subscripts cha , pol and non represent the charged, polar and non-polar groups on the protein molecular surface, respectively, which interact with water molecules differently.…”

Section: Interpretation Of Compressibilitymentioning

confidence: 99%

“…calculated the unit compressibility contributions of charged, cha γ , polar, pol γ , and non-polar, non γ , protein surface area from 18 °C to 55 °C in aqueous solutions. The negative values of unit compressibility contributions shown in Table 2.1 indicate that the interaction between the solvent (23) molecules and proteins contributes negatively to the protein compressibility properties (Gekko and Noguchi, 1979;Gekko and Hasegawa, 1986;Gekko and Hasegawa, 1989;Gekko and Yamagami, 1991;Kharakoz, 1991;Kharakoz and Sarvazyan, 1993;Paci and Marchi, 1996;Kharakoz, 1997;Heremans and Smeller, 1998;Gekko, 2002;Taulier and Chalikian, 2002;Valdez et al, 2001;Chalikian, 2003;Gekko et al, 2003;Marchi, 2003;Gekko et al, 2004;Bano and Marek, 2006;Dadarlat and Post, 2006;Mori et al, 2006). pol γ -66 ± 3 -62 ± 3 -60 ± 3 -58 ± 3 -57 ± 3 non γ -13 ± 2 -9 ± 2 -6 ± 2 -5 ± 2 -4 ± 2 compared the unit compressibility contribution of charged, cha γ , polar, pol γ , and non-polar, non γ , protein surfaces with those on low-molecular-mass compounds to illustrate the hydration properties of proteins.…”

Section: Interpretation Of Compressibilitymentioning

confidence: 99%

Solvent effects on the molecular structures of crude gliadins as revealed by density and ultrasound velocity measurements

Zhang

Scanlon

2011

Journal of Cereal Science

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Decomposition of Protein Experimental Compressibility into Intrinsic and Hydration Shell Contributions

Cited by 53 publications

References 57 publications

Interplay between Hydration and Electrostatic Attraction in Ligand Binding: Direct Observation of Hydration Barrier at Reverse Micellar Interface

Interplay between Hydration and Electrostatic Attraction in Ligand Binding: Direct Observation of Hydration Barrier at Reverse Micellar Interface

Contribution of Water to Pressure and Cold Denaturation of Proteins

Solvent effects on the molecular structures of crude gliadins as revealed by density and ultrasound velocity measurements

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