Osmolyte-induced protein folding free energy changes.

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 carboxyamidated 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 degrees C, the commonly used LEM can lead to false values of DeltaG[stackD-->N0] 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/F0 to F/F0extrap = 1.0 and require that the denatured-state baseline have this value as its intercept. By so doing, the 0%-100% scale-corrected DeltaG[D-->N0] values of RCAM-T1 folding in the presence of various osmolytes are then found to be identical, with small error, demonstrating that DeltaG[D-->N0] 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.

Thermal behavior of HeLa and KB cells in suspension and attached to glass.

HeLa S-3 and KB cells were grown in a LKB Batch Microcalorimeter under a variety of nutrient medium conditions amd mixing intervals. These conditions produced rather large apparent endothermic and exothermic responses on mixing that could be correlated with the presence of suspended cells (unattached) as well as cells attached to the glass calorimeter vessel. Cells capable of being resuspended upon mixing of the calorimeter vessel produces first an endothermic followed by an exothermic signal while attached cells produced only an apparent endothermic response. The exothermic response is believed to be associated with increased metabolic heat on suspending the cells followed by partial suppression of the steady state metabolic heat on cell settling. Rates of cell settling correlated well with the rate of decay of the exothermic signal. The rapid appearance of endothermicity on mixing suggests it is associated with rapid events such as binding of nutrients to cell surfaces. The response in the endothermic direction on mixing is discussed in terms of the disruption of mechanisms which tend to exclude nutrients from the surface of the cell.

The osmophobic effect: natural selection of a thermodynamic force in protein folding.

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.

Osmolyte effects on kinetics of FKBP12 C22A folding coupled with prolyl isomerization.

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.

The paradox between m values and deltaCp's for denaturation of ribonuclease T1 with disulfide bonds intact and broken.

Urea-induced denaturations of RNase T1 and reduced and carboxyamidated RNase T1 (RTCAM) as a function of temperature were analyzed using the linear extrapolation method, and denaturation m values, deltaCp, deltaH, deltaS, and deltaG quantities were determined. Because both deltaCp and m values are believed to reflect the protein surface area newly exposed on denaturation, the prediction is that the ratio of m values for RNase T1 and RTCAM should equal the deltaCp ratio for the two proteins. This is not the case, for it is found that the m value of RTCAM is 1.5 times that of RNase T1, while the denaturation deltaCp's for the two proteins are identical. The paradox of why the two parameters, m and deltaCp, are not equivalent in their behavior is of importance in the interpretations of their respective molecular-level meanings. It is found that the measured denaturation deltaCp's are consistent with deltaCp's calculated on the basis of empirical relationships between the change in surface area on denaturation (deltaASA), and that the measured m value of RNase T1 agrees with m calculated from empirical data relating m to deltaASA. However, the measured m of RTCAM is so much out of line with its calculated m as to call into question the validity of always equating m with surface area newly exposed on denaturation.

The unfolding enthalpy of the pH 4 molten globule of apomyoglobin measured by isothermal titration calorimetry.

The unfolding enthalpy of the pH 4 molten globule from sperm whale apomyoglobin has been measured by isothermal titration calorimetry, using titration to acid pH. The unfolding enthalpy is close to zero at 20 degrees C, in contrast both to the positive values expected for peptide helices and the negative values reported for holomyoglobin and native apomyoglobin. At 20 degrees C, the hydrophobic interaction should make only a small contribution to the unfolding enthalpy according to the liquid hydrocarbon model. Our result indicates that some factor present in the unfolding enthalpies of native proteins makes the unfolding enthalpy of the pH 4 molten globule less positive than expected from data for peptide helices.

Efficacy of macromolecular crowding in forcing proteins to fold.

The intrinsically unstructured protein, reduced and carboxyamidated RNase T1 (TCAM) was used to determine the degree to which macromolecular crowding agents increase the equilibrium constant for folding. TCAM is not catalytically active in an aqueous assay system alone, but becomes catalytically active on addition of 400 mg/ml dextran 70. The activity observed accounts for approximately 16% of the total available TCAM in solution. We interpret this result to mean that 16% of the TCAM becomes folded protein in the presence of the 400 mg/ml dextran 70, and this translates into an approximately five-fold increase in the equilibrium constant for folding. Sarcosine-induced folding of TCAM was performed in the presence of 0, 100, 200 and 300 mg/ml dextran 70, and apparent deltaG(o)(N-D) values determined from the linear extrapolation method provide an estimated 22% folded TCAM formed in the limit of zero sarcosine concentration and in presence of 400 mg/ml dextran 70. The increase in TCAM folding equilibrium constant using this method of determination is approximately 7.5-fold. Overall, the results indicate that macromolecular crowding agents are only modestly effective in promoting folding of this intrinsically unstructured protein.

The Gibbs conference on biothermodynamics: origins and evolution.

The Gibbs conference on biothermodynamics arose in the late 1980's as a 'self-organized' endeavor by researchers at eleven institutions of the US. Over a period of 10 years these annual conferences have grown steadily in size. They have fostered the development of new thermodynamic approaches and their applications in biochemistry. By emphasizing participation by students and postdoctoral fellows they have contributed significantly to the career development of young scientists in this field.

Calorimetric determination of linkage effects involving an acyl-enzyme intermediate.

Enthalpy changes of alpha-chymotrypsin acylation by 3-(2-furyl)acryloylimidazole (FAI) were calorimetrically determined as a function of pH. By observing the functional dependence of acylation enthalpies on buffer ionization heats, a complex pH profile was obtained describing proton release accompanying formation of acyl-enzyme. A pKa of 4.0 for FAI ionization and apparent pKa values of 6.8, 7.55 and 8.8 on the enzyme were used to account for the proton release data. A model which accounts for the proton release behavior was used to fit the acylation enthalpy data and values for the apparent dissociation enthalpies of the groups involved were obtained along with a pH-independent intrinsic enthalpy of acylation. This model suggests a group with an apparent pK = 6.8 and delta Hion = 8.7 kcal/mol which is perturbed to a pK of 7.55 and delta Hion = 7.6 kcal/mol on attachment of the acyl moiety to the enzyme. The apparent ionization enthalpy change for the active-inactive transition (pK3 = 8.8; delta H = 3.0 kcal/mol) corresponds with that calculated from the data of Fersht (J. Mol. Biol. 64 (1972) 497). The pH-independent intrinsic enthalpy of acylation (delta H = -7.9 kcal/mol) is corrected for group ionizations linked to the acylation process. Consequently, it more closely reflects molecular processes of interest such as substrate binding, covalent bond rearrangement, and product release.

Effects of naturally occurring osmolytes on protein stability and solubility: issues important in protein crystallization.

Protein solubility and stability are issues of consideration in attempts to crystallize proteins. These two properties of proteins are also at issue in the cells of organisms that have adapted to water stress conditions that could ordinarily denature or inactivate some proteins. Most organisms that have adapted to environmental stresses have done so by production and accumulation of certain small organic molecules, known as osmolytes, that arose by natural selection and have the ability to stabilize intracellular proteins against the environmental stress. Here, concepts developed to understand the special properties of the naturally occurring osmolytes in effecting protein stability and solubility, and the principles that have come from studies of these compounds have been presented. Along with excluded volume and preferential interaction parameters, identification of the osmophobic effect and the attenuation of this effect by favorable interactions of solute with side-chains appear to contribute to the full set of effects protecting osmolytes have on protein stability and solubility. With these concepts in mind and the fact that urea interacts favorably with the peptide backbone we note that: (1) osmolyte-induced effects on protein stability ranging from denaturation to forcing proteins to fold can be achieved experimentally and the underlying principles understood at near molecular-level detail, and (2) osmolyte-mediated solubility effects ranging from protein precipitation to protein solubilization are predictable based on these principles. These effects are contrasted and compared with effects of 2-methyl-2,4-pentanediol and polyethylene glycol on proteins, and how the principles found for the naturally occurring osmolytes can be applied to these two commonly used protein crystallizing agents.

Covalent bond changes as a driving force in enzyme catalysis.

A procedure is developed for assessing covalent and noncovalent aspects of the acylation of alpha-chymotrypsin (alpha-Ct) by the substrate trifluoroethyl furoate (S) to form furoyl-chymotrypsin (F-Ct) and trifluoroethanol (P1). The free energy change (-4.31 kcal/mol) for the acylation at pH 7, alpha-Ct+S <--> F-Ct+P1, contains contributions from covalent bond changes as well as noncovalent changes. The noncovalent changes are considered to be manifested in the structures of alpha-Ct and F-Ct, and a noncovalent free energy difference between alpha-Ct and F-Ct has been evaluated from the difference in unfolding free energy changes for these proteins. The unfolding free energy changes demonstrate that F-Ct is 1.6 kcal/mol less stable than alpha-Ct at pH7. Thus, despite an overall favorable free energy change for acyl-enzyme formation (-4.31 kcal/mol), covalent linkage of the furoyl moiety to the active site is thermodynamically destabilizing to the enzyme. The consequence of this unfavorable effect of the furoyl moiety on the noncovalent free energy is that "binding" of the covalently linked furoyl moiety cannot be the driving force for acylation. The source of free energy driving acylation is the covalent bond-breaking and bond-making involved in transesterification of the furoyl group to the enzyme. Since the (noncovalent) Michaelis complex between alpha-Ct and substrate is significantly more stable (thermodynamically) than F-Ct, a substantial amount of noncovalent free energy must be given up on forming F-Ct. The destabilization residing in F-Ct is consistent with the possibility that energy transduction occurs when the Michaelis complex is converted to F-Ct and that destabilization is relieved on reaching the next activated complex.

How valid are denaturant-induced unfolding free energy measurements? Level of conformance to common assumptions over an extended range of ribonuclease A stability.

A thermodynamic cycle is used to explore a host of assumptions, conditions, and criteria which must be met for evaluation of authentic unfolding free energy changes. The thermodynamic cycle involves measurement of the unfolding free energy change (delta GzeroN-U) for RNase A at a reference pH, along with determination of the titration free energy changes for the native and unfolded species over an extended pH range. From these free energy changes, delta GzeroN-U at any pH in the range can be predicted and compared with delta GzeroN-U determined by use of the linear extrapolation method (LEM). Good agreement is found between predicted and determined free energy changes covering a broad range of protein stability changes (5 kcal/mol), pH (pH from 3 to 8.5), and lengths of linear extrapolation (C1/2 values from 2.4 to 7.7 M urea). The agreement between predicted and LEM-determined delta GzeroN-U values demonstrates (1) that delta GzeroN-U determined by the LEM is a function of state; i.e., it has the properties of additivity and independence of pathway required of an authentic free energy quantity; (2) the ability to obtain delta GzeroN-U values which are in agreement with the free energy change predicted by the cycle is independent of the length of linear extrapolation; and (3) the two-state assumption holds over an extensive pH range. The fact that the pH titration curve of unfolded RNase A in 6 M GdnHCl could be used in accurately predicting urea-induced delta GzeroN-U values shows that the unfolded ensemble in 6 M GdnHCl is thermodynamically identical to urea-unfolded RNase A as far as the pH dependence of protein stability is concerned. Urea-induced and GdnHCl-induced RNase A delta GzeroN-U values at pH 3 were found not to agree with one another, but this appears to be due to the inability to control the salt effect of GdnHCl on the native state of RNase A. These results provide strong evidence that the LEM applied to urea-induced unfolding of RNase A results in reliable free energy changes that meet a number of essential criteria for authentic thermodynamic quantities. The titration method is important in its own right in providing a means for evaluating the pH dependence of two-state protein unfolding free energy changes which does not require analysis of denaturant-induced unfolding transitions.

Monitoring the sizes of denatured ensembles of staphylococcal nuclease proteins: implications regarding m values, intermediates, and thermodynamics.

Fluorescence and size-exclusion chromatography (SEC) are used to monitor urea denaturation of wild-type staphylococcal nuclease (SN) as well as the m+ and m- mutants A69T and V66W, respectively. It is found that the SEC partition coefficient, 1/Kd, is directly proportional to the Stokes radii of proteins. From the Stokes radii, the denatured ensembles of the three proteins are found to be highly compact in the limit of low urea concentration and expand significantly with increasing urea concentration. The m values from fluorescence-detected denaturation of the SN proteins are generally considered to reflect the relative sizes of denatured ensembles. However, the rank order of m values of the SN proteins studied do not correspond to the rank order of denatured ensemble sizes detected by 1/Kd, suggesting that m values reflect more than just surface area increases on denaturation. SEC provides two complementary ways to demonstrate the existence of intermediates in urea denaturation and illustrates that V66W undergoes a three-state transition. Fluorescence-detected urea denaturations of A69T and wt SN do not correspond with 1/Kd-detected denaturation profiles, a result that would ordinarily mean that the transitions are non-two-state. However, this interpretation fails to recognize the rapidly changing size and thermodynamic character of the denatured ensembles of these proteins both within and outside of the transition zone. The implications of the changing sizes and thermodynamic character of the denatured ensembles for SN proteins are manifold, requiring a reconsideration of the thermodynamics of proteins whose denatured ensembles behave as those of SN proteins.

The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes.

Transfer free energy measurements of amino acids from water to the osmolytes, sucrose and sarcosine, were made as a function of osmolyte concentration. From these data, transfer free energies of the amino acid side chains were obtained, and the transfer free energy of the peptide backbone was determined from solubility measurements of diketopiperazine (DKP). Using static accessible surface evaluations of the native and unfolded states of ribonuclease A, solvent exposed side chain and peptide backbone areas were multiplied by their transfer free energies and summed in order to evaluate the transfer free energy of the native and unfolded states of the protein from water to the osmolyte solutions. The results reproduced the main features of the free energy profile determined for denaturation of proteins in the presence of osmolytes. The side chains were found collectively to favor exposure to the osmolyte in comparison to exposure in water, and in this sense the side chains favor protein unfolding. The major factor which opposes and overrides the side chain preference for denaturation and results in the stabilization of proteins observed in osmolytes is the highly unfavorable exposure of polypeptide backbone on unfolding. Except for urea and guanidine hydrochloride solutions, it is shown that all organic solvents (e.g., dioxane, ethanol, ethylene glycol) and solutes (osmolytes) for which transfer free energy measurements have been determined exhibit unfavorable transfer free energy of the peptide backbone.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of proline on lactate dehydrogenase activity: testing the generality and scope of the compatibility paradigm.

The k(cat) and K(m) kinetic parameters of the labile enzyme rabbit muscle lactic dehydrogenase were determined as a function of the concentration of proline, a solute (osmolyte) accumulated in the cells of many organisms to protect them against environmental stresses. Proline is believed to protect against the stress(es) without altering the functional activity of cellular macromolecules, a property defining it as a "compatible osmolyte." In the range of 0-2 M proline, K(cat) and K(m) values for both substrates are essentially unchanged, but between 2 M and 4 M proline, k(cat) decreases by a factor of 3 to 4, whereas K(m) values are only modestly changed, if at all. These results are consistent with the proposal that compatible osmolytes do not affect functional activity, that the property of compatibility expressed by such osmolytes is generic without regard to the evolutionary history of the protein, and that the organic osmolyte concentration range over which compatibility is exhibited is extensive. In short, the results are in full accord with the principal hypothesis of "compatible osmolytes" in detail and scope.