How does sucrose stabilize the native state of globular proteins?

Graziano, Giuseppe

doi:10.1016/j.ijbiomac.2011.10.025

Cited by 36 publications

(62 citation statements)

References 54 publications

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“…Using our theoretical methods based on statistical mechanics wherein the solvent-entropy effect is highlighted, we have investigated protein folding, 33 cold [14][15][16] and pressure [21][22][23][24] denaturating of a protein, and sugar-induced enhancement of the protein thermal stability. 30 The crucial importance of the solvent entropy in protein folding and denaturation has also been pointed out in studies using the classical scaled particle theory, 13,27 though the physical interpretations are significantly different from ours.…”

Section: Introductionmentioning

confidence: 60%

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

Oshima

Kinoshita

2015

The Journal of Chemical Physics

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In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient values, however, the many-body correlation plays significant roles in the β-sheet formation and argument of relative stabilities of very similar structures of a protein. These results are argued in detail with respect to the four physically insightful constituents and the two factors mentioned above. The relevance to the absence or presence of hydrogen-bonding properties in the solvent is also discussed in detail.

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Section: Introductionmentioning

confidence: 60%

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

Oshima

Kinoshita

2015

The Journal of Chemical Physics

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“…This analysis also indicates that more attention to packing effects is needed. For example, Graziano has shown, using scaled particle theory, that one can explain the protein-stabilizing effect of the small molecule sucrose through packing changes (9).…”

Section: Discussionmentioning

confidence: 99%

“…The volume between big crowding molecules is also filled with small crowding molecules! More than 20 y ago Berg argued that water must be included (7), but with rare exceptions (8,9) his work was ignored. More realistic schematics of the chemical potential and dimerization reactions are shown in Fig.…”

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confidence: 99%

Analysis of the size dependence of macromolecular crowding shows that smaller is better

Sharp

2015

Proc. Natl. Acad. Sci. U.S.A.

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The aqueous milieu inside cells contains as much as 30-40% dissolved protein and RNA by volume. This large concentration of macromolecules is expected to cause significant deviations from solution ideality. In vivo biochemical reaction rates and equilibria might differ significantly from those measured in the majority of in vitro experiments that are performed at much lower macromolecule concentrations. Consequently crowding, a nonspecific phenomenon believed to arise from the large excluded volume of these macromolecules, has been studied extensively by experimental and theoretical methods. However, the relevant theory has not been applied consistently. When the steric effects of macromolecular crowders and small molecules like water and ions are treated on an equal footing, the effect of the macromolecules is opposite to that commonly believed. Large molecules are less effective at crowding than water and ions. There is also a surprisingly weak dependence on crowder size. Molecules of medium size, ∼5 Å radius, have the same effect as much larger macromolecules like proteins and RNA. These results require a reassessment of observed high-concentration effects and of strategies to mimic in vivo conditions with in vitro experiments. T he milieu inside cells contains a large amount of solutes that include small ions, metabolites, and macromolecules. Typical protein/RNA concentrations range from 300 mg/mL to 400 mg/mL or about 30-40% by weight. These are 10-fold or more higher than the macromolecular concentrations usually encountered in in vitro measurements and could lead to significant nonideality in solution behavior. The possibility that in vivo biochemical reaction rates and equilibria might be quite different from measured values due to this nonideality has stimulated considerable research. Macromolecular crowding in particular has stimulated a large number of studies, which have been extensively reviewed (1-5). Crowding has been variously described as physical occupation of volume by the macromolecules, which is then unavailable to other molecules, as an excluded volume effect, as a nonspecific effect due to steric repulsion, and as eliminating positions at which the protein can be placed (2, 5, 6). The other contribution to nonideality is from interactions between various solution components, either attractive or repulsive-repulsive interactions distinct from the van der Waals core repulsion or steric factor underlying crowding. We know very little about the contribution of intersolute interactions to nonideality in vivo. Crowding has been more extensively studied because the steric or excluded volume of a macromolecule is a welldefined property, it is always present, and its qualitative effect on biochemical reactions seems obvious (2). However, as I demonstrate in this paper, the effect of crowding macromolecules on a biochemical reaction is not obvious, the relevant theory has not been consistently applied, and indeed the effect is opposite to that commonly believed.Analyses of the effect of crowding mac...

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“…If this is increased, excluded volume effects grow larger (8,10). This provides one explanation for the quite different effects Smith et al (2) see for the crowding agents dextran, Ficoll, and PEG vs. proteins.…”

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confidence: 96%

Unpacking the origins of in-cell crowding

Sharp

2016

Proc. Natl. Acad. Sci. U.S.A.

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The living cell, the fundamental unit of biological organization, was discovered in its apparent simplicity by van Leeuwenhoek in the 17th century. Scientists since then have continued to unpack nested levels of amazingly complex cellular structure and organization, right down to the atomic level. However, one of the cell's simplest properties is not yet understood, perhaps even misunderstood. The interior of the cell contains a high concentration of dissolved solutes, principally ions, metabolites, proteins, and RNA. In a word, it is crowded in there. Estimates range from 30% to 40% by volume occupied by protein and RNA solutes, depending on the cell type and compartment (1). Biochemists and biophysicists have long been concerned that these high concentrations impart significantly nonideal solution behavior. The vast majority of measurements of equilibria and rates have been made in vitro. Although the ionic strength, osmolality, pH, and redox potential environment inside the cell can be matched with suitable buffers, the concern is that the effects of the macromolecular solutes, principally protein and RNA, are not accounted for. The crucial and currently unanswered questions are, How relevant is the plethora of in vitro experiments to in vivo conditions? Are measured equilibrium constants, rates, and other thermodynamic data significantly different? If so, by how much and in what direction? In principle one can address this directly by in vivo measurements, but the experiments are difficult, and the answers have been slow in coming. In PNAS Smith et al. (2), by measuring a protein folding equilibrium in vivo, now provide some answers-and they are surprising.To appreciate the surprise, it is helpful to briefly touch on the more than three-decade history of the macromolecular crowding field. The notable feature of macromolecules as cosolvents that is missing from simple buffers is their size. All molecules in solution effectively exclude each other; they cannot overlap, due to what is termed the hard-core or van der Waals repulsion. An early pioneer in this field, Minton (3), explicitly emphasized "excluded volume as a determinant of macromolecular structure and reactivity," whereas Ellis (4) stressed the "obvious" aspect of this, meaning that a large excluded volume is a property of all macromolecules. An extensive review covers much of the subsequent literature (5). Of course, solutes can cause nonideal behavior through a second mechanism, strong intermolecular interactions such as electrostatic and hydrophobic effects. Although crowding is now often used as a synonym for any effects of concentrated solutes, for the purpose of this commentary I will take crowding to refer to the excluded volume effects, as originally defined (3, 4), because disentangling size effects and interaction effects is precisely where the advances of Smith et al. (2) lie. I also discuss effects on equilibria only. Given our recently revised understanding of equilibrium effects, it seems premature to discuss the more complex effects of...

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How does sucrose stabilize the native state of globular proteins?

Cited by 36 publications

References 54 publications

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

Analysis of the size dependence of macromolecular crowding shows that smaller is better

Unpacking the origins of in-cell crowding

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