Role of solvent properties of aqueous media in macromolecular crowding effects

Abstract

Analysis of the macromolecular crowding effects in polymer solutions show that the excluded volume effect is not the only factor affecting the behavior of biomolecules in a crowded environment. The observed inconsistencies are commonly explained by the so-called soft interactions, such as electrostatic, hydrophobic, and van der Waals interactions, between the crowding agent and the protein, in addition to the hard nonspecific steric interactions. We suggest that the changes in the solvent properties of aqueous media induced by the crowding agents may be the root of these "soft" interactions. To check this hypothesis, the solvatochromic comparison method was used to determine the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions of different polymers (dextran, poly(ethylene glycol), Ficoll, Ucon, and polyvinylpyrrolidone) with the polymer concentration up to 40% typically used as crowding agents. Polymer-induced changes in these features were found to be polymer type and concentration specific, and, in case of polyethylene glycol (PEG), molecular mass specific. Similarly sized polymers PEG and Ucon producing different changes in the solvent properties of water in their solutions induced morphologically different α-synuclein aggregates. It is shown that the crowding effects of some polymers on protein refolding and stability reported in the literature can be quantitatively described in terms of the established solvent features of the media in these polymers solutions. These results indicate that the crowding agents do induce changes in solvent properties of aqueous media in crowded environment. Therefore, these changes should be taken into account for crowding effect analysis.

Observed crowding effects on Mycobacterium tuberculosis 2-trans-enoyl-ACP (CoA) reductase enzyme activity are not due to excluded volume only

“…However, as the intracellular components are heterogeneous with respect to shape, size and possible macromolecular chemical interactions, in vitro experiments will never perfectly mimic the physiological in vivo milieu. It has been proposed that quinary structure should be implemented into models to study protein function in the crowded cellular environment 54 , and that polymer-induced changes in the solvent properties of aqueous media should be taken into account 55 . As “soft” interactions were invoked to explain the results for PEG 6000 and only sucrose showed a decrease in both k cat / K m for NADH and k cat for DD-CoA, the results presented in our manuscript do not unequivocally meet the criteria for crowding effect due to exclude volume only.…”

Peculiarities of the Super-Folder GFP Folding in a Crowded Milieu

“…This further supports the idea that, in addition to the excluded volume, some additional factors are involved in the modulation of the behavior of sfGFP in the crowded milieu. Accumulated experimental data including results obtained in this study indicate that crowding agents may affect the solvent properties of aqueous solutions in different manners, depending on the crowding agent macromolecule structure and the concentration [33,34,55]. These solvent properties are the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions [55].…”

“…Accumulated experimental data including results obtained in this study indicate that crowding agents may affect the solvent properties of aqueous solutions in different manners, depending on the crowding agent macromolecule structure and the concentration [33,34,55]. These solvent properties are the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions [55]. The diverse impact of different polymers on the solvent properties of water leads to the unequal changes of the protein properties in the crowded environment modeled by these polymers.…”

Analyzing the effects of protecting osmolytes on solute–water interactions by solvatochromic comparison method: I. Small organic compounds

“…39 Sorbitol effect is not as pronounced but is quite noticeable too, since the solvent dipolarity/polarizability of water in its solution at concentration of 2.0 M is similar to that of dextran-75 and Ficoll-70 at concentrations of 40% wt. 39 The above data indicate that all the osmolytes under consideration alter solvent properties of water in their solutions in the osmolyte-specific manner (except identical effects displayed by sucrose and trehalose). The HBD acidity of water, α, is also affected by osmolytes, as illustrated by Figure 1C.…”

“…The observed effects are similar for sucrose and trehalose, and these effects are quite significant. 39 All osmolytes increase the water HBA basicity, β, as shown in Figure 1B. 39 Sorbitol effect is not as pronounced but is quite noticeable too, since the solvent dipolarity/polarizability of water in its solution at concentration of 2.0 M is similar to that of dextran-75 and Ficoll-70 at concentrations of 40% wt.…”