Viscosity dependence of O2 escape from respiratory proteins as a function of cosolvent molecular weight

Yedgar, Saul; Tétreau, Catherine; Gavish, Benjamin; Lavalette, Daniel

doi:10.1016/s0006-3495(95)80227-4

Cited by 57 publications

(111 citation statements)

References 27 publications

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“…Thus, n exit is largest and k exit is smallest in the fully hydrated protein. The conclusion is consistent with experiments by Yedgar and coworkers (26). The temperature dependence of folding from the collapsed state of cytochrome c at constant viscosity also supports the arguments given here.…”

Section: Fractional Viscosity Dependence Of Protein Motionssupporting

confidence: 93%

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Protein folding is slaved to solvent motions

Frauenfelder

Fenimore

Chen

et al. 2006

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

272

281

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Proteins, the workhorses of living systems, are constructed from chains of amino acids, which are synthesized in the cell based on the instructions of the genetic code and then folded into working proteins. The time for folding varies from microseconds to hours. What controls the folding rate is hotly debated. We postulate here that folding has the same temperature dependence as the ␣-fluctuations in the bulk solvent but is much slower. We call this behavior slaving. Slaving has been observed in folded proteins: Large-scale protein motions follow the solvent fluctuations with rate coefficient k␣ but can be slower by a large factor. Slowing occurs because large-scale motions proceed in many small steps, each determined by k␣. If conformational motions of folded proteins are slaved, so a fortiori must be the motions during folding. The unfolded protein makes a Brownian walk in the conformational space to the folded structure, with each step controlled by k␣. Because the number of conformational substates in the unfolded protein is extremely large, the folding rate coefficient, kf, is much smaller than k␣. The slaving model implies that the activation enthalpy of folding is dominated by the solvent, whereas the number of steps nf ‫؍‬ k␣͞kf is controlled by the number of accessible substates in the unfolded protein and the solvent. Proteins, however, undergo not only ␣-but also ␤-fluctuations. These additional fluctuations are local protein motions that are essentially independent of the bulk solvent fluctuations and may be relevant at late stages of folding.folding energy landscape ͉ fractional viscosity dependence ͉ internal viscosity ͉ Maxwell relation ͉ protein-solvent interaction P roteins in cells fold and unfold continuously. Consequently, an understanding of folding rates is key. The distribution and strength of contacts in the native state is one ingredient that influences the rate of folding (1). A second ingredient is the effect of the solvent, because protein motions are intimately linked to the motions of the environment. Our slaving model quantifies the linkage. The model is based on three concepts: Proteins assume a large number of different conformations or substates (2), their organization is described by a hierarchic energy landscape (3), and large-scale protein fluctuations follow the ␣-relaxation (Debye or dielectric relaxation) in the bulk solvent (4-6). Here we propose that these concepts also are valid for folding and that they lead to the model pictured in Fig. 1. Fig. 1a is a cartoon of folding and a 1D cross-section through the high-dimensional energy landscape. Fig. 1b is a 2D cross-section.

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Section: Fractional Viscosity Dependence Of Protein Motionssupporting

confidence: 93%

“…Different solvents can interact differently with the protein and its hydration shell and can change the dynamic and static properties and, in particular, the stability (19,20,(24)(25)(26)(27)(28)(29). Fig.…”

Section: Fractional Viscosity Dependence Of Protein Motionsmentioning

confidence: 99%

Protein folding is slaved to solvent motions

Frauenfelder

Fenimore

Chen

et al. 2006

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

272

281

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“…But also for example for the O 2 escape from respiratory proteins, an inverse correlation between the viscogen molecular weight and its effectiveness at slowing dynamics has been found. 4,13 In a sense, solvent viscosity might be considered just a measure of the concentration of viscogen molecules, and indeed, plotting the averaged time τ 2 against sucrose concentration rather than solvent viscosity reveals a linear dependence up to 40% w/w sucrose concentration (Fig. 6(b)).…”

Section: Merging Experimental and MD Resultsmentioning

confidence: 99%

“…For example, the viscosity inside the cellular cytoplasm can differ by greater than ten fold, varying across the type of cell (and species), its life stage, and locally within the cell or organelle. 2 Other studies on this topic have measured the viscosity dependence of small ligand dissociation 3,4 or the folding rates of peptides or of entire proteins. [5][6][7][8][9][10][11][12][13][14] Viscosity has an obvious important role in diffusive processes within the cell, but may also have an additional important role in regulating reaction rates and metabolism.…”

Section: Introductionmentioning

confidence: 99%

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

Waldauer

Stucki-Buchli

Frey

et al. 2014

The Journal of Chemical Physics

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By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein.The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations. By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein. The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations. © 2014 AIP Publishing LLC.

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“…Viscosity dependence of enzymatic and protein (ligand binding/rebinding) reactions is a long standing problem for biophysics [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19]. For such reactions the functional dependence of the reaction rate constant for the rate limiting stage k on solvent viscosity η has the form…”

Section: Introductionmentioning

confidence: 99%

Model for solvent viscosity effect on enzymatic reactions

Sitnitsky

2010

Chemical Physics

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Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon have not led to consensus among researches about its origin. They invoke to either a modification of 1. the conventional Kramers' theory or that of 2. the Stokes law. We show that there is an alternative interpretation of the phenomenon at which neither of these modifications is in fact indispensable. Basing on an analogy from the theory of adsorption on heterogeneous surfaces we reconcile 1. and 2. with the experimentally observable dependence. We assume that an enzyme solution in solvent with or without cosolvent molecules is an ensemble of samples with different values of the viscosity for the movement of the system along the reaction coordinate. We assume that this viscosity consists of the contribution with the weight q from cosolvent molecules and that with the weight 1− q from protein matrix and solvent molecules. We introduce heterogeneity in our system with the help of a distribution over the weight q. The function of the distribution is a unique characteristic of the solution of enzymes (type of the enzyme, cosolvent molecular weight, pH, temperature, etc.). We verify the obtained solution of the integral equation for the unknown function of the distribution by direct substitution. We conclude that even at linear relationship between the solvent viscosity and that for the movement of the system along the reaction coordinate our approach enables us to obtain the required dependence. All parameters of the model are related to experimentally observable values. The meaning of fractional exponents appears to be the characteristic for the behavior of the distribution with the variation of the weight q. Our approach yields the existence of the limit value for the fractional power exponent with the decrease of cosolvent molecular weight that is in agreement experimental data known from the literature. This limit value is determined by the properties of the protein structure and thus is a unique characteristic of the type of the enzyme only rather than that of the solution. General formalism is exemplified by the analysis of literature experimental data for oxygen escape from hemerythin.

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Viscosity dependence of O2 escape from respiratory proteins as a function of cosolvent molecular weight

Cited by 57 publications

References 27 publications

Protein folding is slaved to solvent motions

Protein folding is slaved to solvent motions

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

Model for solvent viscosity effect on enzymatic reactions

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