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Jorg Rosgen - One of the best experts on this subject based on the ideXlab platform.
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preferential solvation: Osmolyte solvation of proteins, aminoacids, and peptides
2020Co-Authors: Matthew T Auton, D. Wayne Bolen, Jorg RosgenAbstract:Protein stability and solubility depend strongly on the presence of Osmolytes, because of the protein preference to be solvated by either water or Osmolyte. It has traditionally been assumed that only this relative preference can be measured, and that the individual solvation contributions of water and Osmolyte are inaccessible. However, it is possible to determine hydration and Osmolyte solvation (osmolation) separately using Kirkwood-Buff theory, and this fact has recently been utilized by several researchers. Here, we provide a thermodynamic assessment of how each surface group on proteins contributes to the overall hydration and osmolation. Our analysis is based on transfer free energy measurements with model-compounds that were previously demonstrated to allow for a very successful prediction of Osmolyte-dependent protein stability. When combined with Kirkwood-Buff theory, the Transfer Model provides a space-resolved solvation pattern of the peptide unit, amino acids, and the folding/unfolding equilibrium of proteins in the presence of Osmolytes. We find that the major solvation effects on protein side-chains originate from the Osmolytes, and that the hydration mostly depends on the size of the side-chain. The peptide backbone unit displays a much more variable hydration in the different Osmolyte solutions. Interestingly, the presence of sucrose leads to simultaneous accumulation of both the sugar and water in the vicinity of peptide groups, resulting from a saccharide accumulation that is less than the accumulation of water, a net preferential exclusion. Only the denaturing Osmolyte, urea, obeys the classical solvent exchange mechanism in which the preferential interaction with the peptide unit excludes water.
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synergy in protein Osmolyte mixtures
Journal of Physical Chemistry B, 2015Co-Authors: Jorg RosgenAbstract:Virtually all taxa use Osmolytes to protect cells against biochemical stress. Osmolytes often occur in mixtures, such as the classical combination of urea with TMAO (trimethylamine N-oxide) in cartilaginous fish or the cocktail of at least six different Osmolytes in the kidney. The concentration patterns of Osmolyte mixtures found in vivo make it likely that synergy between them plays an important role. Using statistical mechanical n-component Kirkwood–Buff theory, we show from first principles that synergy in protein–Osmolyte systems can arise from two separable sources: (1) mutual alteration of protein surface solvation and (2) effects mediated through bulk Osmolyte chemical activities. We illustrate both effects in a four-component system with the experimental example of the unfolding of a notch ankyrin domain in urea–TMAO mixtures, which make urea a less effective denaturant and TMAO a more effective stabilizer. Protein surface effects are primarily responsible for this synergy. The specific patterns ...
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Distinctive Solvation Patterns Make Renal Osmolytes Diverse
Biophysical Journal, 2013Co-Authors: Ruby Jackson-atogi, Prem Kumar Sinha, Jorg RosgenAbstract:The kidney uses mixtures of five Osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the Osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, including solubility data for scyllo-inositol. It turns out that renal Osmolytes fall into three distinct classes with respect to their solvation. Trimethyl-amines (GPC and glycine-betaine) are characterized by strong hard-sphere-like self-exclusion; urea, taurine, and myo-inositol have a tendency toward self-association; sorbitol and most other nonrenal Osmolytes have a relatively constant, intermediate solvation that has components of both exclusion and association. The data presented here show that renal Osmolytes are quite diverse with respect to their solvation patterns, and they can be further differentiated based on observations from experiments examining their effect on macromolecules. It is expected, based on the available surface groups, that each renal Osmolyte has distinct effects on various classes of biomolecules. This likely allows the kidney to use specific combinations of Osmolytes independently to fine-tune the chemical activities of several types of molecules.
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Osmolyte effects on protein stability and solubility a balancing act between backbone and side chains
Biophysical Chemistry, 2011Co-Authors: Matthew Auton, Luis Marcelo F Holthauzen, Jorg Rosgen, Mikhail Sinev, Wayne D BolenAbstract:In adaptation biology the discovery of intracellular Osmolyte molecules that in some cases reach molar levels, raises questions of how they influence protein thermodynamics. We've addressed such questions using the premise that from atomic coordinates, the transfer free energy of a native protein (ΔGtr, N) can be predicted by summing measured water-to-Osmolyte transfer free energies of the protein's solvent exposed side chain and backbone component parts. ΔGtr, D is predicted using a self avoiding random coil model for the protein, and ΔGtr, D − ΔGtr, N, predicts the m-value, a quantity that measures the Osmolyte effect on the N ⇌ D transition. Using literature and newly measured m-values we show 1:1 correspondence between predicted and measured m-values covering a range of 12 kcal/mol/M in protein stability for 46 proteins and 9 different Osmolytes. Osmolytes present a range of side chain and backbone effects on N and D solubility and protein stability key to their biological roles.
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structural thermodynamics of protein preferential solvation Osmolyte solvation of proteins aminoacids and peptides
Proteins, 2008Co-Authors: Matthew Auton, Wayne D Bolen, Jorg RosgenAbstract:Protein stability and solubility depend strongly on the presence of Osmolytes, because of the protein preference to be solvated by either water or Osmolyte. It has traditionally been assumed that only this relative preference can be measured, and that the individual solvation contributions of water and Osmolyte are inaccessible. However, it is possible to determine hydration and Osmolyte solvation (osmolation) separately using Kirkwood-Buff theory, and this fact has recently been utilized by several researchers. Here, we provide a thermodynamic assessment of how each surface group on proteins contributes to the overall hydration and osmolation. Our analysis is based on transfer free energy measurements with model-compounds that were previously demonstrated to allow for a very successful prediction of Osmolyte-dependent protein stability. When combined with Kirkwood-Buff theory, the Transfer Model provides a space-resolved solvation pattern of the peptide unit, amino acids, and the folding/unfolding equilibrium of proteins in the presence of Osmolytes. We find that the major solvation effects on protein side-chains originate from the Osmolytes, and that the hydration mostly depends on the size of the side-chain. The peptide backbone unit displays a much more variable hydration in the different Osmolyte solutions. Interestingly, the presence of sucrose leads to simultaneous accumulation of both the sugar and water in the vicinity of peptide groups, resulting from a saccharide accumulation that is less than the accumulation of water, a net preferential exclusion. Only the denaturing Osmolyte, urea, obeys the classical solvent exchange mechanism in which the preferential interaction with the peptide unit excludes water. Proteins 2008. © 2008 Wiley-Liss, Inc.
Shekhar Garde - One of the best experts on this subject based on the ideXlab platform.
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Osmolyte trimethylamine n oxide does not affect the strength of hydrophobic interactions origin of Osmolyte compatibility
Biophysical Journal, 2005Co-Authors: Manoj V. Athawale, Jonathan S Dordick, Shekhar GardeAbstract:Osmolytes are small organic solutes accumulated at high concentrations by cells/tissues in response to osmotic stress. Osmolytes increase thermodynamic stability of folded proteins and provide protection against denaturing stresses. The mechanism of Osmolyte compatibility and Osmolyte-induced stability has, therefore, attracted considerable attention in recent years. However, to our knowledge, no quantitative study of Osmolyte effects on the strength of hydrophobic interactions has been reported. Here, we present a detailed molecular dynamics simulation study of the effect of the Osmolyte trimethylamine-N-oxide (TMAO) on hydrophobic phenomena at molecular and nanoscopic length scales. Specifically, we investigate the effects of TMAO on the thermodynamics of hydrophobic hydration and interactions of small solutes as well as on the folding-unfolding conformational equilibrium of a hydrophobic polymer in water. The major conclusion of our study is that TMAO has almost no effect either on the thermodynamics of hydration of small nonpolar solutes or on the hydrophobic interactions at the pair and many-body level. We propose that this neutrality of TMAO toward hydrophobic interactions—one of the primary driving forces in protein folding—is at least partially responsible for making TMAO a “compatible” Osmolyte. That is, TMAO can be tolerated at high concentrations in organisms without affecting nonspecific hydrophobic effects. Our study implies that protein stabilization by TMAO occurs through other mechanisms, such as unfavorable water-mediated interaction of TMAO with the protein backbone, as suggested by recent experimental studies. We complement the above calculations with analysis of TMAO hydration and changes in water structure in the presence of TMAO molecules. TMAO is an amphiphilic molecule containing both hydrophobic and hydrophilic parts. The precise balance of the effects of hydrophobic and hydrophilic segments of the molecule appears to explain the virtual noneffect of TMAO on the strength of hydrophobic interactions.
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Osmolyte trimethylamine-N-oxide does not affect the strength of hydrophobic interactions: Origin of Osmolyte compatibility
Biophysical Journal, 2005Co-Authors: Manoj V. Athawale, Jonathan S Dordick, Shekhar GardeAbstract:Osmolytes are small organic solutes accumulated at high concentrations by cells/tissues in response to osmotic stress. Osmolytes increase thermodynamic stability of folded proteins and provide protection against denaturing stresses. The mechanism of Osmolyte compatibility and Osmolyte-induced stability has, therefore, attracted considerable attention in recent years. However, to our knowledge, no quantitative study of Osmolyte effects on the strength of hydrophobic interactions has been reported. Here, we present a detailed molecular dynamics simulation study of the effect of the Osmolyte trimethylamine-N-oxide (TMAO) on hydrophobic phenomena at molecular and nanoscopic length scales. Specifically, we investigate the effects of TMAO on the thermodynamics of hydrophobic hydration and interactions of small solutes as well as on the folding-unfolding conformational equilibrium of a hydrophobic polymer in water. The major conclusion of our study is that TMAO has almost no effect either on the thermodynamics of hydration of small nonpolar solutes or on the hydrophobic interactions at the pair and many-body level. We propose that this neutrality of TMAO toward hydrophobic interactions-one of the primary driving forces in protein folding-is at least partially responsible for making TMAO a "compatible" Osmolyte. That is, TMAO can be tolerated at high concentrations in organisms without affecting nonspecific hydrophobic effects. Our study implies that protein stabilization by TMAO occurs through other mechanisms, such as unfavorable water-mediated interaction of TMAO with the protein backbone, as suggested by recent experimental studies. We complement the above calculations with analysis of TMAO hydration and changes in water structure in the presence of TMAO molecules. TMAO is an amphiphilic molecule containing both hydrophobic and hydrophilic parts. The precise balance of the effects of hydrophobic and hydrophilic segments of the molecule appears to explain the virtual noneffect of TMAO on the strength of hydrophobic interactions. © 2005 by the Biophysical Society.
D W Bolen - One of the best experts on this subject based on the ideXlab platform.
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an analysis of the molecular origin of Osmolyte dependent protein stability
Protein Science, 2007Co-Authors: Jorg Rosgen, Bernard Pettitt, D W BolenAbstract:Protein solvation is the key determinant for isothermal, concentration-dependent effects on protein equilibria, such as folding. The required solvation information can be extracted from experimental thermodynamic data using Kirkwood-Buff theory. Here we derive and discuss general properties of proteins and Osmolytes that are pertinent to their biochemical behavior. We find that hydration depends very little on Osmolyte concentration and type. Strong dependencies on both Osmolyte concentration and type are found for Osmolyte self-solvation and protein–Osmolyte solvation changes upon unfolding. However, solvation in Osmolyte solutions does not involve complex concentration dependencies as found in organic molecules that are not used as Osmolytes in nature. It is argued that the simple solvation behavior of naturally occurring Osmolytes is a prerequisite for their usefulness in osmotic regulation in vivo.
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An analysis of the molecular origin of Osmolyte‐dependent protein stability
Protein Science, 2007Co-Authors: Jorg Rosgen, Bernard Pettitt, D W BolenAbstract:Protein solvation is the key determinant for isothermal, concentration-dependent effects on protein equilibria, such as folding. The required solvation information can be extracted from experimental thermodynamic data using Kirkwood-Buff theory. Here we derive and discuss general properties of proteins and Osmolytes that are pertinent to their biochemical behavior. We find that hydration depends very little on Osmolyte concentration and type. Strong dependencies on both Osmolyte concentration and type are found for Osmolyte self-solvation and protein–Osmolyte solvation changes upon unfolding. However, solvation in Osmolyte solutions does not involve complex concentration dependencies as found in organic molecules that are not used as Osmolytes in nature. It is argued that the simple solvation behavior of naturally occurring Osmolytes is a prerequisite for their usefulness in osmotic regulation in vivo.
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Osmolyte-induced protein folding free energy changes
Proteins, 2006Co-Authors: Peng Wu, D W BolenAbstract:Upon addition of protecting Osmolyte to an aqueous solution of an intrinsically unstructured protein, spectral observables are often seen to change in a sigmoid fashion as a function of increasing Osmolyte concentration. Commonly, such data are analyzed using the linear extrapolation model (LEM), a method that defines a scale from 0%-100% folded species at each Osmolyte concentration by means of extending pre- and post-folding baselines into the transition region. Defining the 0%-100% folding scale correctly for each Osmolyte is an important part of the analysis, leading to evaluation of the fraction of folded protein existing in the absence of Osmolytes. In this study, we used reduced and carboxy-amidated RNase T1 (RCAM-T1) as an intrinsically unstructured protein, and determined the thermodynamic stability of RCAM-T1 induced by naturally occurring Osmolytes. Because the folded fraction of the protein population determined by experiments of thermal and urea-induced denaturation is nonzero in the absence of Osmolytes at 15°C, the commonly used LEM can lead to false values of ΔG 0 D→N for protein folding due to the arbitrary assumption that the protein is 100% unfolded in the presence of buffer alone. To correct this problem, titration of the protein solution with urea and extrapolating back to zero urea concentration gives the spectral value for 100% denatured protein. With fluorescence as the observable we redefine F/F 0 to F/F extrap 0 = 1.0 and require that the denatured-state baseline have this value as its intercept. By so doing, the 0%-100% scale-corrected ΔG 0 D→N values of RCAM-T1 folding in the presence of various Osmolytes are then found to be identical, with small error, demonstrating that ΔG 0 D→N is independent of the Osmolytes used. Such a finding is an important step in validating this quantity derived from the LEM as having the properties expected of an authentic thermodynamic parameter. The rank order of Osmolyte efficacies in stabilizing RCAM-T1 is sarcosine > sucrose > sorbitol > proline >betaine > glycerol.
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Osmolyte effects on kinetics of fkbp12 c22a folding coupled with prolyl isomerization
Journal of Molecular Biology, 2003Co-Authors: Andrew T Russo, Jorg Rosgen, D W BolenAbstract:Unfolding and refolding kinetics of human FKBP12 C22A were monitored by fluorescence emission over a wide range of urea concentration in the presence and absence of protecting Osmolytes glycerol, proline, sarcosine and trimethylamine-N-oxide (TMAO). Unfolding is well described by a mono-exponential process, while refolding required a minimum of two exponentials for an adequate fit throughout the urea concentration range considered. The bi-exponential behavior resulted from complex coupling between protein folding, and prolyl isomerization in the denatured state in which the urea-dependent rate constant for folding was greater than, equal to, and less than the rate constants for prolyl isomerization within the urea concentration range of zero to five molar. Amplitudes and the observed folding and unfolding rate constants were fitted to a reversible three-state model composed of two sequential steps involving the native state and a folding-competent denatured species thermodynamically linked to a folding-incompetent denatured species. Excellent agreement between thermodynamic parameters for FKBP12 C22A folding calculated from the kinetic parameters and those obtained directly from equilibrium denaturation assays provides strong support for the applicability of the mechanism, and provides evidence that FKBP12 C22A folding/unfolding is two-state, with prolyl isomer heterogeneity in the denatured ensemble. Despite the chemical diversity of the protecting Osmolytes, they all exhibit the same kinetic behavior of increasing the rate constant of folding and decreasing the rate constant for unfolding. Osmolyte effects on folding/unfolding kinetics are readily explained in terms of principles established in understanding Osmolyte effects on protein stability. These principles involve the osmophobic effect, which raises the Gibbs energy of the denatured state due to exposure of peptide backbone, thereby increasing the folding rate. This effect also plays a key role in decreasing the unfolding rate when, as is often the case, the activated complex exposes more backbone than is exposed in the native state.
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the osmophobic effect natural selection of a thermodynamic force in protein folding
Journal of Molecular Biology, 2001Co-Authors: D W Bolen, Ilia V BaskakovAbstract:Abstract Intracellular organic Osmolytes are present in certain organisms adapted to harsh environments and these Osmolytes protect intracellular macromolecules against the denaturing environmental stress. In natural selection of organic Osmolytes as protein stabilizers, it appears that the Osmolyte property selected for is the unfavorable interaction between the Osmolyte and the peptide backbone, a solvophobic thermodynamic force that we call the osmophobic effect. Because the peptide backbone is highly exposed to Osmolyte in the denatured state, the osmophobic effect preferentially raises the free energy of the denatured state, shifting the equilibrium in favor of the native state. By focusing the solvophobic force on the denatured state, the native state is left free to function relatively unfettered by the presence of Osmolyte. The osmophobic effect is a newly uncovered thermodynamic force in nature that complements the well-recognized hydrophobic interactions, hydrogen bonding, electrostatic and dispersion forces that drive protein folding. In organisms whose survival depends on the intracellular presence of Osmolytes that can counteract denaturing stresses, the osmophobic effect is as fundamental to protein folding as these well-recognized forces.
Gary M Smith - One of the best experts on this subject based on the ideXlab platform.
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three transporters mediate uptake of glycine betaine and carnitine by listeria monocytogenes in response to hyperosmotic stress
Applied and Environmental Microbiology, 2003Co-Authors: Apostolos S Angelidis, Gary M SmithAbstract:The uptake and accumulation of the potent Osmolytes glycine betaine and carnitine enable the food-borne pathogen Listeria monocytogenes to proliferate in environments of elevated osmotic stress, often rendering salt-based food preservation inadequate. To date, three Osmolyte transport systems are known to operate in L. monocytogenes: glycine betaine porter I (BetL), glycine betaine porter II (Gbu), and a carnitine transporter OpuC. We investigated the specificity of each transporter towards each Osmolyte by creating mutant derivatives of L. monocytogenes 10403S that possess each of the transporters in isolation. Kinetic and steady-state Osmolyte accumulation data together with growth rate experiments demonstrated that osmotically activated glycine betaine transport is readily and effectively mediated by Gbu and BetL and to a lesser extent by OpuC. Osmotically stimulated carnitine transport was demonstrated for OpuC and Gbu regardless of the nature of stressing salt. BetL can mediate weak carnitine uptake in response to NaCl stress but not KCl stress. No other transporter in L. monocytogenes 10403S appears to be involved in osmotically stimulated transport of either Osmolyte, since a triple mutant strain yielded neither transport nor accumulation of glycine betaine or carnitine and could not be rescued by either Osmolyte when grown under elevated osmotic stress.
Manoj V. Athawale - One of the best experts on this subject based on the ideXlab platform.
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Osmolyte trimethylamine n oxide does not affect the strength of hydrophobic interactions origin of Osmolyte compatibility
Biophysical Journal, 2005Co-Authors: Manoj V. Athawale, Jonathan S Dordick, Shekhar GardeAbstract:Osmolytes are small organic solutes accumulated at high concentrations by cells/tissues in response to osmotic stress. Osmolytes increase thermodynamic stability of folded proteins and provide protection against denaturing stresses. The mechanism of Osmolyte compatibility and Osmolyte-induced stability has, therefore, attracted considerable attention in recent years. However, to our knowledge, no quantitative study of Osmolyte effects on the strength of hydrophobic interactions has been reported. Here, we present a detailed molecular dynamics simulation study of the effect of the Osmolyte trimethylamine-N-oxide (TMAO) on hydrophobic phenomena at molecular and nanoscopic length scales. Specifically, we investigate the effects of TMAO on the thermodynamics of hydrophobic hydration and interactions of small solutes as well as on the folding-unfolding conformational equilibrium of a hydrophobic polymer in water. The major conclusion of our study is that TMAO has almost no effect either on the thermodynamics of hydration of small nonpolar solutes or on the hydrophobic interactions at the pair and many-body level. We propose that this neutrality of TMAO toward hydrophobic interactions—one of the primary driving forces in protein folding—is at least partially responsible for making TMAO a “compatible” Osmolyte. That is, TMAO can be tolerated at high concentrations in organisms without affecting nonspecific hydrophobic effects. Our study implies that protein stabilization by TMAO occurs through other mechanisms, such as unfavorable water-mediated interaction of TMAO with the protein backbone, as suggested by recent experimental studies. We complement the above calculations with analysis of TMAO hydration and changes in water structure in the presence of TMAO molecules. TMAO is an amphiphilic molecule containing both hydrophobic and hydrophilic parts. The precise balance of the effects of hydrophobic and hydrophilic segments of the molecule appears to explain the virtual noneffect of TMAO on the strength of hydrophobic interactions.
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Osmolyte trimethylamine-N-oxide does not affect the strength of hydrophobic interactions: Origin of Osmolyte compatibility
Biophysical Journal, 2005Co-Authors: Manoj V. Athawale, Jonathan S Dordick, Shekhar GardeAbstract:Osmolytes are small organic solutes accumulated at high concentrations by cells/tissues in response to osmotic stress. Osmolytes increase thermodynamic stability of folded proteins and provide protection against denaturing stresses. The mechanism of Osmolyte compatibility and Osmolyte-induced stability has, therefore, attracted considerable attention in recent years. However, to our knowledge, no quantitative study of Osmolyte effects on the strength of hydrophobic interactions has been reported. Here, we present a detailed molecular dynamics simulation study of the effect of the Osmolyte trimethylamine-N-oxide (TMAO) on hydrophobic phenomena at molecular and nanoscopic length scales. Specifically, we investigate the effects of TMAO on the thermodynamics of hydrophobic hydration and interactions of small solutes as well as on the folding-unfolding conformational equilibrium of a hydrophobic polymer in water. The major conclusion of our study is that TMAO has almost no effect either on the thermodynamics of hydration of small nonpolar solutes or on the hydrophobic interactions at the pair and many-body level. We propose that this neutrality of TMAO toward hydrophobic interactions-one of the primary driving forces in protein folding-is at least partially responsible for making TMAO a "compatible" Osmolyte. That is, TMAO can be tolerated at high concentrations in organisms without affecting nonspecific hydrophobic effects. Our study implies that protein stabilization by TMAO occurs through other mechanisms, such as unfavorable water-mediated interaction of TMAO with the protein backbone, as suggested by recent experimental studies. We complement the above calculations with analysis of TMAO hydration and changes in water structure in the presence of TMAO molecules. TMAO is an amphiphilic molecule containing both hydrophobic and hydrophilic parts. The precise balance of the effects of hydrophobic and hydrophilic segments of the molecule appears to explain the virtual noneffect of TMAO on the strength of hydrophobic interactions. © 2005 by the Biophysical Society.