Decrease In Solvent-excluded Volume Research Articles

On the Stabilizing Effect of Aspartate and Glutamate and Its Counteraction by Common Denaturants.

By performing differential scanning calorimetry(DSC) measurements on RNase A, we studied the stabilization provided by the addition of potassium aspartate(KAsp) or potassium glutamate (KGlu) and found that it leads to a significant increase in the denaturation temperature of the protein. The stabilization proves to be mainly entropic in origin. A counteraction of the stabilization provided by KAsp or KGlu is obtained by adding common denaturants such as urea, guanidinium chloride, or guanidinium thiocyanate. A rationalization of the experimental data is devised on the basis of a theoretical approach developed by one of the authors. The main contribution to the conformational stability of globular proteins comes from the gain in translational entropy of water and co-solute ions and/or molecules for the decrease in solvent-excluded volume associated with polypeptide folding (i.e., there is a large decrease in solvent-accessible surface area). The magnitude of this entropic contribution increases with the number density and volume packing density of the solution. The two destabilizing contributions come from the conformational entropy of the chain, which should not depend significantly on the presence of co-solutes, and from the direct energetic interactions between co-solutes and the protein surface in both the native and denatured states. It is the magnitude of the latter that discriminates between stabilizing and destabilizing agents.

On the Molecular Driving Force of Protein–Protein Association

The amount of water-accessible-surface-area, WASA, buried upon protein–protein association is a good measure of the non-covalent complex stability in water; however, the dependence of the binding Gibbs free energy change upon buried WASA proves to be not trivial. We assign a precise physicochemical role to buried WASA in the thermodynamics of non-covalent association and perform close scrutiny of the contributions favoring and those contrasting protein–protein association. The analysis indicates that the decrease in solvent-excluded volume, an entropic effect, described by means of buried WASA, is the molecular driving force of non-covalent association in water.

Shape effect on non-covalent dimer stability using classic scaled particle theory

The shape of two non-covalent dimers formed by different variants of the B1 domain of protein G plays an important role for their stability in water and aqueous solutions [Proc. Natl. Acad. Sci. U.S.A. 115 (2018) 10965]. I demonstrate how much the stabilization afforded by the decrease in solvent-excluded volume upon association depends on the shape of the dimers in water and aqueous sugar solutions, using classic scaled particle theory. There is a strong dependence upon the decrease in water accessible surface area associated with dimer formation, whose general significance deserves attention.

Why does urea have a different effect on the collapse temperature of PDEAM and PNIPAM?

The two polymers poly(N,N-diethylacrylamide), PDEAM, and poly(N-isopropylacrylamide), PNIPAM, undergo a coil-to-globule collapse transition in water on increasing the temperature. The process is endothermic and it is driven by the gain in translational entropy of water molecules due to the decrease in solvent-excluded volume associated with the transition from swollen to globular conformations of the polymer. Curiously, in the presence of urea, the two polymers have a different behaviour: globular conformations are stabilized for PNIPAM, while swollen conformations are stabilized for PDEAM [Macromolecules 49 (2016) 234]. Here, we present an application of the theoretical approach already used to rationalize several aspects of PNIPAM collapse [Phys. Chem. Chem. Phys. 17 (2015) 27750; Phys. Chem. Chem. Phys. 18 (2016) 14426]. This model is able to provide a reliable explanation for the different behaviour of urea towards PDEAM and PNIPAM. The difference might be in fact due to the number of urea-polymer contacts that is larger in the case of PDEAM with respect to PNIPAM for the presence of two extra methylene groups in each side chain of the former polymer.

Comment on "Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors" by A. Battisti, G. Ciasca, A. Grottesi and A. Tenenbaum, Phys. Chem. Chem. Phys., 2017, 19, 8435.

In a recent article, A. Battisti et al., Phys. Chem. Chem. Phys., 2017, 19, 8435, results from SAXS measurements, metadynamic trajectories and classic MD trajectories at different temperatures have been used to study the temperature-induced compaction of the intrinsically disordered protein tau. The analysis, though technically sound, does not provide a clear explanation of hydrophobic interaction strengthening on increasing the temperature and its relationship with the population increase of secondary structural elements. Actually, hydrophobic interaction is driven by the gain in translational entropy of water molecules associated with the decrease in solvent-excluded volume due to chain compaction. The magnitude of this solvent-excluded volume effect increases with temperature in water because the density of water is almost temperature-independent due to the strength of H-bonds. Since α-helix formation leads to a significant decrease in the solvent-excluded volume, the connection with hydrophobic interaction and chain compaction emerges directly.

Hydrostatic pressure effect on hydrophobic hydration and pairwise hydrophobic interaction of methane

At room temperature, the Ben-Naim standard hydration Gibbs energy of methane is a positive quantity that increases markedly with hydrostatic pressure [M. S. Moghaddam and H. S. Chan, J. Chem. Phys. 126, 114507 (2007)]. This finding is rationalized by showing that the magnitude of the reversible work to create a suitable cavity in water increases with pressure due to both the increase in the volume packing density of water and the contribution of the pressure-volume work. According to the present approach, at room temperature, the Gibbs energy of the contact-minimum configuration of two methane molecules is a negative quantity that increases in magnitude with hydrostatic pressure. This result is not in line with the results of several computer simulation studies [T. Ghosh, A. E. Garcia, and S. Garde, J. Am. Chem. Soc. 123, 10997-11003 (2001)], and emerges because pairwise association causes a decrease in solvent-excluded volume that produces a gain of configurational/translational entropy of water molecules, whose magnitude increases with the volume packing density of the liquid phase.

On the signature of the hydrophobic effect at a single molecule level

Li and Walker [Proc. Natl. Acad. Sci. U. S. A., 2011, 108, 16527-16532] have been able to obtain the Gibbs energy change associated with the unfolding + extension of collapsed conformations of single hydrophobic chains in water, by means of atomic force microscopy measurements. These Gibbs energy changes show parabolic temperature profiles, considered to be a signature of the hydrophobic effect, and whose maximum depends on the size of monomer side chains. It has now been shown that these Gibbs energy changes can be reproduced in a more-than-qualitative manner by means of a theoretical approach developed to rationalize the temperature dependence of the conformational stability of globular proteins [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. The marked decrease in solvent-excluded volume associated with the transition from extended conformations to collapsed ones is the physical ground of the hydrophobic effect and plays the pivotal role. It is partially counterbalanced by the entropy loss upon collapse associated with the internal rotation degrees of freedom of monomer side chains. The same approach is able to account for the results obtained for the unfolding + extension of collapsed conformations of single polystyrene chains in ethanol-water solutions.

Reply to the comment by Setny, Baron and McCammon on the article “Molecular driving forces of the pocket-ligand hydrophobic association”, Chem. Phys. Lett. 533 (2012) 95

I reply to a comment by Setny, Baron and McCammon on a study of mine, published in Chem. Phys. Lett. 533 (2012) 95, in which I provided an alternative explanation of the results obtained by the above authors [J. Chem. Theory Comput. 6 (2010) 2866] for the concave pocket-convex ligand hydrophobic association. I re-emphasize that: (a) the reorganization of water–water H-bonds associated with pocket and ligand dewetting, characterized by an exact enthalpy–entropy compensation, does not affect the binding Gibbs energy change and cannot be the driving force of the process; (b) the decrease in solvent-excluded volume plays a fundamental role.

Role of salts on the strength of pairwise hydrophobic interaction

The strengthening of pairwise hydrophobic interaction upon salt addition to water is due to the increased number density of aqueous salt solutions, according to scaled particle theory. Two CH 4 molecules occupy the same volume both when they are far apart and when they are in contact, however, the contact configuration is favoured because the solvent-excluded volume decreases upon association and there is a substantial gain of translational entropy of solvent molecules. The same decrease in solvent-excluded volume upon association causes a different entropy gain depending on the number density of the solution: the larger the number density, the larger will be the number of solvent particles that gain translational freedom.