The stability of globular proteins

Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease

The nucleases A produced by two strains of Staphylococcus aureus, which have different stabilities, differ only in the identity of the single amino acid at residue 124. The nuclease from the Foggi strain of S. aureus (by convention nuclease WT), which contains His124, is 1.9 kcal.mol-1 less stable (at pH 5.5 and 20 degrees C) than the nuclease from the V8 strain (by convention nuclease H124L), which contains Leu124. In addition, the population of the trans conformer at the Lys116-Pro117 peptide bond, as observed by NMR spectroscopy, is different for the two variants: about 15% for nuclease WT and 9% for nuclease H124L. In order to improve our understanding of the origin of these differences, we compared the properties of WT and H124L with those of the H124A and H124I variants. We discovered a correlation between effects of different residues at this position on protein stability and on stabilization of the cis configuration of the Lys116-Pro117 peptide bond. In terms of free energy, approximately 17% of the increase in protein stability manifests itself as stabilization of the cis configuration at Lys116-Pro117. This result implies that the differences in stability arise mainly from structural differences between the cis configurational isomers at Pro117 of the different variants at residue 124. We solved the X-ray structure of the cis form of the most stable variant, H124L, and compared it with the published high-resolution X-ray structure of the cis form of the most stable variant, WT (Hynes TR, Fox RO, 1991, Proteins Struct Funct Genet 10:92-105). The two structures are identical within experimental error, except for the side chain at residue 124, which is exposed in the models of both variants. Thus, the increased stability and changes in the trans/cis equilibrium of the Lys116-Pro117 peptide bond observed in H124L relative to WT are due to subtle structural changes that are not observed by current structure determination technique. Residue 124 is located in a helix. However, the stability changes are too large and follow the wrong order of stability to be explained simply by differences in helical propensity. A second site of conformational heterogeneity in native nuclease is found at the His46-Pro47 peptide bond, which is approximately 80% trans in both WT and H124L. Because proline to glycine substitutions at either residue 47 or 117 remove the structural heterogeneity at that position and increase protein stability, we determined the X-ray structures of H124L + P117G and H124L + P47G + P117G and the kinetic parameters of H124L, H124L + P47G, H124L + P117G, and H124L + P47G + P117G. The individual P117G and P47G mutations cause decreases in nuclease activity, with kcat affected more than Km, and their effects are additive. The P117G mutation in nuclease H124L leads to the same local conformational rearrangement described for the P117G mutant of WT (Hynes TR, Hodel A, Fox RO, 1994, Biochemistry 33:5021-5030). In both P117G mutants, the loop formed by residues 112-117 is located closer to the adjacent loop formed by residues 77-85, and residues 115-118 adopt a type I' beta-turn conformation with the Lys116-Gly117 peptide bond in the trans configuration, as compared with the parent protein in which these residues have a typeVIa beta-turn conformation with the Lys116-Pro117 peptide bond in the cis configuration. Addition of the P47G mutation appears not to cause any additional structural changes. However, the electron density for part of the loop containing this peptide bond was not strong enough to be interpreted.

Influence of glycerol on the structure and stability of ferric horse heart myoglobin: a SAXS and circular dichroism study

The influence of glycerol on the structural properties of Fe(III)-horse heart myoglobin has been investigated by absorbance, CD and SR-SAXS spectroscopy. The results obtained indicate that both the tertiary and the secondary (alpha-helix) conformations of the protein are influenced by glycerol; in particular, an increase of approx. 8% in helical content was observed. Further, analysis of both the acid- and guanidine-induced denaturation transitions points to a glycerol-induced decreased stability of the tertiary structure; conversely, the alpha-helix conformation is found to be stabilized by the organic solvent. Finally, the SR-SAXS data show that gyration radius, cross-section and thickness of the protein increase in the presence of the organic solvent; however, the protein maintains a compact state.

Molecular collapse: the rate-limiting step in two-state cytochrome c folding

Experiments with cytochrome c (cyt c) show that an initial folding event, molecular collapse, is not an energetically downhill continuum as commonly presumed but represents a large-scale, time-consuming, cooperative barrier-crossing process. In the absence of later misfold-reorganization barriers, the early collapse barrier limits cyt c folding to a time scale of milliseconds. The collapse process itself appears to be limited by an uphill search for some coarsely determined transition state structure that can nucleate subsequent energetically downhill folding events. An earlier "burst phase" event at strongly native conditions appears to be a non-specific response of the unfolded chain to reduced denaturant concentration. The molecular collapse process may or may not require the co-formation of the amino- and carboxyl-terminal helices, which are present in an initial metastable intermediate directly following the rate-limiting collapse. After the collapse-nucleation event, folding can proceed rapidly in an apparent two-state manner, probably by way of a predetermined sequence of metastable intermediates that leads to the native protein structure (Bai et al., Science 269:192-197, 1995).

The role of helix formation in the folding of a fully alpha-helical coiled coil

To determine when secondary structure forms as two chains coalesce to form an alpha-helical dimer, the folding rates of variants of the coiled coil region of GCN4 were compared. Residues at non-perturbing positions along the exterior length of the helices were substituted one at a time with alanine and glycine to vary helix propensity and therefore dimer stability. For all variants, the bimolecular folding rate remains largely unchanged; the unfolding rate changes to largely account for the change in stability. Thus, contrary to most folding models, widespread helix is not yet formed at the rate-limiting step in the folding pathway. The high-energy transition state is a collapsed form that contains little if any secondary structure, as suggested for the globular protein cytochrome c (Sosnick et al., Proteins 24: 413-426, 1996).

Future directions in folding: the multi-state nature of protein structure

All possible protein folding intermediates exist in equilibrium with the native protein at native as well as non-native conditions, with occupation determined by their free energy level. The study of these forms can illuminate the fundamental principles of protein structure and folding. Hydrogen exchange methods can be used to detect and characterize these partially unfolded forms at native conditions and as a function of mild denaturant and temperature. This information illuminates the requirements that govern the ability of kinetic and equilibrium methods to study folding intermediates.

The development of tertiary interactions during the folding of a large protein

BACKGROUND

We have used protein engineering and relaxation kinetics to examine the order in which secondary structure elements assemble during folding. Aliphatic contacts in the core of a large domain within the monomeric protein phosphoglycerate kinase (PGK) were disrupted in order to map the development of interactions between beta-strand and alpha-helix residues, both near and distant in the sequence.

RESULTS

Mutations which break sequence-local alpha-beta contacts destabilize the first identifiable intermediate in folding, showing that these contacts develop early in the folding pathway. In contrast, the removal of sequence-distant alpha-beta interactions has little effect at this stage, but reduces the rate at which the intermediate converts to the native state. Thus, contacts between these remote segments of secondary structure start to form later on in the process, during the rate-limiting transition.

CONCLUSIONS

In the case of this large protein domain, our results support the hypothesis that folding proceeds by a hierarchic pathway. Interactions form rapidly between sequence-local groups to produce microdomains before the establishment of the long-range contacts necessary to define the global fold, which proceeds through a highly hydrated transition state.

Susceptibility of beta-lactoglobulin and sodium caseinate to proteolysis by pepsin and trypsin

The susceptibility of beta-LG and sodium caseinate to proteolysis by pepsin and trypsin was investigated using SDS or urea-PAGE. The effects were studied of heat, urea, and 2-mercaptoethanol on proteolysis. Native beta-LG was resistant to hydrolysis by pepsin or trypsin because of its compact globular structure. Heat treatment of beta-LG solutions at 90 to 100 degrees C for 5 or 10 min caused changes in the structure or conformation of the protein that rendered it accessible to pepsin and enhanced the extent of proteolysis by trypsin. The susceptibility of beta-LG to proteolysis by pepsin was markedly increased in the presence of urea (3 to 6 M), and the effect was reversible after removal of urea by dialysis. Proteolysis by trypsin was also increased by the presence of 2% 2-mercaptoethanol. Sodium caseinate was very accessible to pepsin without pretreatment and was extensively hydrolyzed at pH 1 to 5 in the presence of 5 M urea (which prevented the protein from precipitation in the isoelectric region); optimal pH was about 2. The activity of pepsin on sodium caseinate at pH 2 was not significantly affected by urea concentration up to about 8 M. The results indicated that the changes in conformation and structure of beta-LG that were induced by heating, reduction, or urea rendered the protein susceptible to peptic hydrolysis.

A review of protein engineering for the food industry

In this review I briefly describe the technique of protein engineering and indicate how the present state of knowledge allows proteins to be mutated to increase or decrease stability. I discuss experiments on both model proteins and those of relevance to the food industry and show how hydrophobic forces are a major driving force for folding as well as having a major role in thermostability. I also indicate the large contribution that hydrogen bonding, electrostatic interactions and, in a less well predicted way, disulfide bridges make to thermostability.

Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding

Denaturant m values, the dependence of the free energy of unfolding on denaturant concentration, have been collected for a large set of proteins. The m value correlates very strongly with the amount of protein surface exposed to solvent upon unfolding, with linear correlation coefficients of R = 0.84 for urea and R = 0.87 for guanidine hydrochloride. These correlations improve to R = 0.90 when the effect of disulfide bonds on the accessible area of the unfolded protein is included. A similar dependence on accessible surface area has been found previously for the heat capacity change (delta Cp), which is confirmed here for our set of proteins. Denaturant m values and heat capacity changes also correlate well with each other. For proteins that undergo a simple two-state unfolding mechanism, the amount of surface exposed to solvent upon unfolding is a main structural determinant for both m values and delta Cp.

Breathing life into the folding pathway of cytochrome c

In cytochrome c, the unfolding reaction occurs in four discreet stops, as monitored by the exchange of solvent hydrogen for backbone aminde hydrogens under varying denaturant concentrations.

Thermal unfolding of the cytotoxin alpha-sarcin: phospholipid binding induces destabilization of the protein structure

The effect of membrane binding on the structure and stability of the cytotoxin alpha-sarcin has been studied by differential scanning calorimetry, Fourier-transform infrared and fluorescence spectroscopic techniques. The thermal unfolding of alpha-sarcin in aqueous solution fits into a two-state transition characterized by a transition temperature (Tm) of 52.6 degrees C and a calorimetric enthalpy (delta Hcal) of 136 kcal/mol. Upon interaction with phosphatidylglycerol vesicles, alpha-sarcin undergoes conformational changes, as deduced from the FTIR and fluorescence emission spectra. These changes result in a decreased Tm and delta Hcal values for the thermal unfolding of phospholipid-bound alpha-sarcin. The lower Tm value for lipid-bound alpha-sarcin is also observed at the level of secondary and tertiary structures, based on analyses of both the amide I' infrared spectrum and the tryptophan emission of the protein as a function of temperature, respectively. The results obtained indicate a protein destabilization promoted by the phospholipid interaction.

Extremely rapid protein folding in the absence of intermediates

Here we used the cold-shock protein CspB from Bacillus subtilis to study protein folding at an elementary level. The thermodynamic stability of this small five-stranded beta-barrel protein is low, but unfolding and refolding are extremely rapid reactions. In 0.6 M urea the time constant of refolding is about 1.5 ms, and at the transition midpoint (4 M urea) the folded and unfolded forms equilibrate in less than 100 ms. Both the equilibrium unfolding transition and the folding kinetics are perfectly described by a N<-->U two-state model. The validity of this model was confirmed by several kinetic tests. Folding intermediates could neither be detected at equilibrium nor in the folding kinetics. We suggest that the extremely rapid folding of CspB and the absence of folding intermediates are related phenomena.

Structural characterization of folded and unfolded states of an SH3 domain in equilibrium in aqueous buffer

The isolated N-terminal Src homology 3 (SH3) domain of Drosophila drk exists in equilibrium between folded and unfolded states in aqueous buffer near neutral pH. Nuclear magnetic resonance spectra recorded on both states simultaneously exhibit an approximate 1:1 ratio of protein conformations. The folded form is similar to other known SH3 structures, especially the N-terminal SH3 domain of the mammalian homologue GRB2. A stretch of sequential amide-amide nuclear Overhauser effect cross-peaks for resonances of the unfolded state is observed in a region corresponding to beta-strands in the folded state. The results suggest that turn-like conformations may be preferentially sampled in the folding pathway for this predominantly beta-structured SH3 domain. In addition, a stable turn at Leu-28 is observed in the unfolded but not in the folded state. Comparison of this unfolded form with a denatured state in 2 M guanidine hydrochloride shows that, while both are highly disordered, these states are not identical and more residual structure is present under nondenaturing conditions.

Stability of subtilisins and related proteinases (subtilases)

The stability towards thermal and chemical (guanidine hydrochloride, GnHCl) denaturation of six inhibited subtilases (mesentericopeptidase, subtilisins BPN', Carlsberg and DY, proteinase K and thermitase) has been investigated by kinetic and equilibrium studies. The unfolding processes were monitored by circular dichroic and fluorescence spectroscopy. Experiments in the absence and presence of extraneous calcium in the concentration range 2 x 10(-3)-10(-1) M were performed. The presence of calcium in the weak calcium binding site changes the denaturation drastically. The heat- (or GnHCl-) induced unfolding curves obtained using CD spectroscopy show two independent transitions which seem not to have been resolved before. The presence of Ca2+ in the second (third in the case of thermitase) binding site increases the Tm values by 11-21 degrees C and the delta GD(H2O) values obtained from denaturation experiments in GnHCl by 6.7-7.2 kcal/mol when an extraneous Ca2+ concentration of 2 x 10(-2) M was used. One interpretation is that the initial step of denaturation in the presence of added calcium is the formation of a partially unfolded intermediate form, retaining a highly ordered structure with 60-85% of the alpha-helix structure of the native enzyme. This intermediate then unfolds at a temperature considerably higher than that of the same proteinases in the absence of added Ca2+. The free energy of stabilization of the intermediates is increased by 1.8-2.8 times in comparison with that for the unfolding reactions of the subtilases with empty Ca2/Ca3 binding sites. A second interpretation is that the two steps in the unfolding curves correspond to enzyme without and with calcium in the weak binding site. Fluorescence experiments confirm the mechanism involving the formation of intermediate states. The results are discussed in relation to the X-ray models of the six subtilases.

Stabilization of a strained protein loop conformation through protein engineering

Staphylococcal nuclease is found in two folded conformations that differ in the isomerization of the Lys 116-Pro 117 peptide bond, resulting in two different conformations of the residue 112-117 loop. The cis form is favored over the trans with an occupancy of 90%. Previous mutagenesis studies have shown that when Lys 116 is replaced by glycine, a trans conformation is stabilized relative to the cis conformation by the release of steric strain in the trans form. However, when Lys 116 is replaced with alanine, the resulting variant protein is identical to the wild-type protein in its structure and in the dominance of the cis configuration. The results of these studies suggested that any nuclease variant with a non-glycine residue at position 116 should also favor the cis form because of steric requirements of the beta-carbon at this position. In this report, we present a structural analysis of four nuclease variants with substitutions at position 116. Two variants, K116E and K116M, follow the "beta-carbon" hypothesis by favoring the cis form. Furthermore, the crystal structure of K116E is nearly identical to that of the wild-type protein. Two additional variants, K116D and K116N, provide exceptions to this simple "beta-carbon" rule in that the trans conformation is stabilized relative to the cis configuration by these substitutions. Crystallographic data indicate that this stabilization is effected through the addition of tertiary interactions between the side chain of position 116 with the surrounding protein and water structure. The detailed trans conformation of the K116D variant appears to be similar to the trans conformation observed in the K116G variant, suggesting that these two mutations stabilize the same conformation but through different mechanisms.

Acid stabilization of human growth hormone equilibrium folding intermediates

Equilibrium denaturation experiments were performed on human growth hormone (hGH) under acidic conditions (pH 1.5-3.0) and different protein concentrations. At 0.1 mg/ml hGH using intrinsic tryptophan fluorescence and far-UV circular dichroism (CD) detection, midpoint values of 4.6 M GdnHCl were observed that are identical to those obtained at neutral pH. However, the delta G values were reduced at pH 2.5 relative to pH 8.0 (10.5 vs. 15 kcal/mol). Increasing the protein concentration to 1 mg/ml resulted in a biphasic denaturation profile by far-UV CD detection at 222 nm, while near-UV CD measurements at 295 nm yielded a cooperative transition with a midpoint value of 3.6 M GdnHCl. These results indicate that equilibrium intermediates having a propensity to aggregate are highly populated under acid conditions. Static light scattering measurements performed under partial unfolding conditions (4.5 M GdnHCl) at pH 2.5 confirmed the existence of a large molecular weight (congruent to 80 kDa) self-associated intermediate. No evidence of aggregation was found for hGH under acid conditions in the absence of denaturant, indicating that self-association results from the formation of an intermediate. Equilibrium GdnHCl concentration-jump experiments confirmed that association only occurs from an intermediate species and not from any other conformational state, and formation of the self-associated intermediate can lead to irreversible loss of protein due to precipitation. These results demonstrate that acid stabilizes equilibrium folding intermediates of hGH.

Denaturation of horseradish peroxidase with urea and guanidine hydrochloride

Favourable effects of urea and guanidine hydrochloride (Gdn HCl) on solubilization of the polar, non-polar and peptide groups of horseradish peroxidase (HRP), an example of a globular protein, provide the driving force for unfolding of HRP, in a reversible two-state process. The intrinsic or conformational stability of HRP at various pH values and temperatures has been estimated by the linear extrapolation method (LEM), a denaturant binding model (DBM) and Tanford's model. There is good agreement between these methods. Tanford's model shows that urea interacts with non-polar groups to a greater extent than Gdn HCl does, whereas Gdn HCl interacts more effectively with the peptide groups of HRP.

Fatty acid binding to bovine serum albumin prevents formation of intermediate during denaturation

Urea-induced denaturation of defatted BSA and BSA containing six mol palmitic acid/mol protein (fatted BSA) has been studied by the techniques of UV difference spectroscopy and fluorescence spectroscopy. The notable differences between the two transitions are a shift in the transition of fatted BSA to a higher urea concentration and a three-state denaturation transition in defatted BSA compared to an apparent two-state denaturation transition in fatted BSA. The stable denaturation intermediate in defatted BSA occurs at 4.5-5.0 M urea, a urea concentration at which denaturation in fatted BSA has not yet started. These results are further supported by the difference spectral results obtained at 4.5 M urea in the two albumin preparations. The occurrence of denaturation intermediate only in defatted BSA and the presence of the two strong fatty-acid-binding sites in domain III lead us to conclude that this domain is relatively unstable in the absence of fatty acids and is responsible for the formation of intermediate.

Urea unfolding of peptide helices as a model for interpreting protein unfolding

To provide a model system for understanding how the unfolding of protein alpha-helices by urea contributes to protein denaturation, urea unfolding was measured for a homologous series of helical peptides with the repeating sequence Ala-Glu-Ala-Ala-Lys-Ala and chain lengths varying from 14 to 50 residues. The dependence of the helix propagation parameter of the Zimm-Bragg model for helix-coil transition theory (s) on urea molarity ([urea]) was determined at 0 degree C with data for the entire set of peptides, and a linear dependence of In s on [urea] was found. The results were fitted by the binding-site model and by the solvent-exchange model for the interaction of urea with the peptides. Each of these thermodynamic models is able to describe the data quite well and we are not able to discern any difference between the ability of each model to fit the data. Thus a linear relation, ln s = ln s0 - (m/RT).[urea], fits the data for alpha-helix unfolding, just as others have found for protein unfolding. When the m value determined here for alpha-helix unfolding is multiplied by the number of helical residues in partly helical protein molecules, the resulting values agree within a factor of 2 with observed m values for these proteins. This result indicates that the interaction between urea and peptide groups accounts for a major part of the denaturing action of urea on proteins, as predicted earlier by some model studies with small molecules.

Effects of drug-binding on the thermal denaturation of human serum albumin

Asymmetric thermograms of defatted albumin, alone and in the presence of two model drugs, have been obtained in phosphate buffers at three pH values. The albumin is less thermally stable in the N form, but is protected by both drugs. The nonsteroidal antiinflammatory benoxaprofen offers more protection than warfarin against thermal denaturation.

Two domains of interaction with calcium binding proteins can be mapped using fragments of calponin

Native calponin is able to bind 2 mol of calcium binding protein (CaBP) per mole calponin. This study extends this observation to define the 2 domains of interaction, one of which is near the actin binding site, and the other in the amino-terminal region of calponin. Also, the first evidence for a differentiation in the response of calponin to interaction with caltropin versus calmodulin is demonstrated. The binding of caltropin to cleavage and recombinant fragments of calponin was determined by 3 techniques: tryptophan fluorescence of the fragments, CD measurements to determine secondary structure changes, and analytical ultracentrifugation. In order to delineate the sites of interaction, 3 fragments of calponin have been studied. From a cyanogen bromide cleavage of calponin, residues 2-51 were isolated. This fragment is shown to bind to CaBPs and the affinity for caltropin is slightly higher than that for calmodulin. A carboxyl-terminal truncated mutant of calponin comprising residues 1-228 (CP 1-228) has been produced by recombinant techniques. Analytical ultracentrifugation has shown that CP 1-228, like the parent calponin, is able to bind 2 mol of caltropin per mol of 1-228 in a Ca(2+)-dependent fashion, indicating that there is a second site of interaction between residues 52-228. Temperature denaturation of the carboxyl-terminal truncated fragment compared with whole calponin show that the carboxyl-terminal region does not change the temperature at which calponin melts; however, there is greater residual secondary structure with whole calponin versus the fragment. A second mutant produced through recombinant techniques comprises residues 45-228 and is also able to bind caltropin, thus mapping the location of the second site of interaction to near the actin binding site.

Purification, bioactivity, and secondary structure analysis of mouse and human macrophage migration inhibitory factor (MIF)

The cytokine macrophage migration inhibitory factor (MIF) has been identified to be secreted by the pituitary gland and the monocyte/macrophage and to play an important role in endotoxic shock. Despite the recent molecular cloning of a human T-cell MIF, characterization of the biochemical and biological properties of this protein has remained incomplete because substantial quantities of purified, recombinant, or native MIF have not been available. We describe the cloning of mouse MIF from anterior pituitary cells (AtT-20) and the purification of native MIF from mouse liver by sequential ion exchange and reverse-phase chromatography. For comparison purposes, human MIF was cloned from the Jurkat T-cell line and also characterized. Mouse and human MIF were highly homologous (90% identity over 115 amino acids). Recombinant mouse and human MIF were expressed in Escherichia coli and purified in milligram quantities by a simple two-step procedure. The molecular weight of native mouse MIF (12.5 kDa monomer) was identical with that of recombinant mouse MIF as assessed by gel electrophoresis and mass spectroscopy. No significant post-translational modifications were detected despite the presence of two potential N-linked glycosylation sites. Recombinant MIF inhibited monocyte migration in a dose-dependent fashion, and both recombinant and native MIF-exhibited comparable biological activities. MIF induced the secretion of tumor necrosis factor-alpha and stimulated nitric oxide production by macrophages primed with interferon-gamma. Circular dichroism spectroscopy revealed that bioactive mouse and human MIF exhibit a highly ordered, three-dimensional structure with a significant percentage of beta-sheet and alpha-helix conformation. Guanidine hydrochloride-induced unfolding experiments demonstrated that MIF is of low to moderate thermodynamic stability. These studies establish the biochemical identity of native and recombinant MIF and provide a first insight into the three-dimensional structural properties of this critical inflammatory mediator.

A kinetic method to evaluate the two-state character of solvent-induced protein denaturation

We present a kinetic method to determine the concentration of native molecules in protein folding transitions. It is based on the observation that frequently native protein molecules unfold slowly when transferred to unfolding conditions, whereas folding intermediates unfold rapidly. The fraction of native molecules in a folding transition can thus be determined by kinetic unfolding assays in a two-step procedure. Aliquots of the protein are first equilibrated at different concentrations of denaturant and then transferred to constant unfolding conditions to determine the amplitude of unfolding. This amplitude is a direct measure for the concentration of native molecules in the sample. The two-state character of a solvent-induced unfolding transition can thus be examined. When the fractional change of a spectral property in a transition follows the decrease in the concentration of the native molecules, as measured by the unfolding assays, then the presence of intermediates that differ from the unfolded protein in this property can be definitely excluded. This test complements the calorimetric test for intermediates in thermal unfolding transitions. By using this method, we show that the NaCl-induced folding transition of the reduced and carboxymethylated form of a variant of ribonuclease T1 is well described by the two-state approximation. In the unfolding of apo-alpha-lactalbumin, the measured profile for the native protein coincides with the fluorescence-detected transition, but not with the transition that is monitored by amide circular dichroism. This confirms that a partially folded intermediate is present in the folding transition of apo-alpha-lactalbumin.

Protein denaturation with guanidine hydrochloride or urea provides a different estimate of stability depending on the contributions of electrostatic interactions

The objective of this study was to address the question of whether or not urea and guanidine hydrochloride (GdnHCl) give the same estimates of the stability of a particular protein. We previously suspected that the estimates of protein stability from GdnHCl and urea denaturation data might differ depending on the electrostatic interactions stabilizing the proteins. Therefore, 4 coiled-coil analogs were designed, where the number of intrachain and interchain electrostatic attractions (A) were systematically changed to repulsions (R): 20A, 15A5R, 10A10R, and 20R. The GdnHCl denaturation data showed that the 4 coiled-coil analogs, which had electrostatic interactions ranging from 20 attractions to 20 repulsions, had very similar [GdnHCl]1/2 values (average of congruent to 3.5 M) and, as well, their delta delta Gu values were very close to 0 (0.2 kcal/mol). In contrast, urea denaturation showed that the [urea]1/2 values proportionately decreased with the stepwise change from 20 electrostatic attractions to 20 repulsions (20A, 7.4 M; 15A5R, 5.4 M; 10A10R, 3.2 M; and 20R, 1.4 M), and the delta delta Gu values correspondingly increased with the increasing differences in electrostatic interactions (20A-15A5R, 1.5 kcal/mol; 20A-10A10R, 3.7 kcal/mol; and 20A-20R, 5.8 kcal/mol). These results indicate that the ionic nature of GdnHCl masks electrostatic interactions in these model proteins, a phenomenon that was absent when the unchanged urea was used. Thus, GdnHCl and urea denaturations may give vastly different estimates of protein stability, depending on how important electrostatic interactions are to the protein.

Contribution to global protein stabilization of the N-capping box in human growth hormone

In this work we have investigated the contribution to protein stability of residues forming the boundaries of alpha-helices. At the N-terminus of helix 2 of human growth hormone there are two residues, Ser71 and Glu74, which form two reciprocal hydrogen bonds between the side chains and the backbone nitrogens of either residue (the N-capping box). In order to evaluate the stabilizing effect of each hydrogen bond, site-directed mutagenesis was employed. In addition, the effect of side-chain negative charge on helix stabilization, via charge dipole interaction, was assessed. Ultraviolet spectroscopy and near- and far-UV CD spectroscopy as well as guanidine hydrochloride protein denaturation were used as assays to monitor the conformational and free energy of stabilization changes induced by the point mutations. The results of these experiments can be summarized as follows: (a) receptor binding studies showed that the tertiary conformation of each mutant was similar to that of the native hormone, (b) far-UV CD spectroscopic analyses showed that the overall alpha-helical content was unchanged in the mutants, (c) UV absorption and CD spectroscopic analyses indicated small alterations in helical packing in those mutants in which the hydrogen bond between the side chain of Ser71 and backbone NH of Glu74 was disrupted, (d) the hydrogen bond involving the side chain of Ser71 contributes at least 1.0 kcal/mol to protein stabilization and has a 2-fold larger stabilizing effect than that of the hydrogen bond involving the Glu74 side chain, and (e) the putative charge-dipole interaction of Glu74 with the alpha-helix dipole does not contribute to the stabilization of the tertiary conformation of human growth hormone.

Ligation alters the pathway of urea-induced denaturation of the catalytic trimer of Escherichia coli aspartate transcarbamylase

We have examined the pathway and energetics of urea-induced dissociation and unfolding of the catalytic trimer (c3) of aspartate transcarbamylase from Escherichia coli at low temperature in the absence and presence of carbamyl phosphate (CP; a substrate), N-(phosphonacetyl)-L-Asp (PALA; a bisubstrate analog), and 2 anionic inhibitors, Cl- and ATP, by analytical gel chromatography supplemented by activity assays and ultraviolet difference spectroscopy. In the absence of active-site ligands and in the presence of ATP, c3 dissociates below 2 M urea into swollen c chains that then gradually unfold from 2 to 6 M urea with little apparent cooperativity. Linear extrapolation to 0 M urea of free energies determined in 3 independent types of experiments yields estimates for delta Gdissociation at 7.5 degrees C of about 7-10 kcal m-1 per interface. delta Gunfolding of dissociated chains when modeled as a 2-state process is estimated to be very small, on the order of -2 kcal m-1. The data are also consistent with the possibility that the unfolding of the dissociated monomer is a 1-state swelling process. In the presence of the ligands CP and PALA, and in the presence of Cl-, c3 dissociates at much higher urea concentrations, and trimer dissociation and unfolding occur simultaneously and apparently cooperatively, at urea concentrations that increase with the affinity of the ligand.

The thermodynamics of solvent exchange

A model for solvation in mixed solvents, which was developed for the free energy and preferential interaction [J. A. Schellman (1987), Biopolymers, Vol. 26, pp. 549-559; (1990), Biophysical Chemistry, Vol. 37, pp. 121-140; (1993), Biophysical Chemistry, Vol. 45, pp. 273-279], is extended in this paper to cover the thermal properties: enthalpy, entropy, and heat capacity. An important result is that the enthalpy of solvation H(ex)2 responds directly to the fraction of site occupation. This differs from the free energy G(ex)2 and preferential interaction gamma 32, which are measures of the excess binding above a random distribution of solvent molecules. In other words, the enthalpy is governed by K while G(ex)2 and gamma 32 are governed by (K-1) where K is the equilibrium constant on a mole fraction scale [Schellman (1987)]. The solvation heat capacity Cpex2 consists of two term: (1) the intrinsic heat capacity of species in solution with no change in composition, and (2) a term that accounts for the change in composition that accompanies solvent exchange. Binding to biological macromolecules is heterogeneous but experimentalists must use binding isotherms that assume the homogeneity of sites. Equations are developed for the interpretation of the experimental parameters (number of sites nexp, equilibrium constant Kexp, and enthalpy, delta hexp), when homogeneous formulas are applied to the heterogeneous case. It is shown that the experimental parameters for the occupation and enthalpy are simple functions of the moments of the distribution of equilibrium constants over the sites. In general, nexp is greater than the true number of sites and Kexp is greater than the average of the equilibrium constants. The free energy and preferential interaction can be fit to a homogeneous formula, but the parameters of the curve are not easily represented in terms of the moments of distributions over the sites. The strengths and deficiencies of this type of thermodynamic model are discussed.

Relative stabilities of synthetic peptide homo- and heterodimeric troponin-C domains

It has previously been shown that synthetic peptides corresponding to calcium-binding sites III (SCIII) and IV (SCIV) from troponin-C can undergo a calcium-induced dimerization to form the respective homodimers (Shaw GS, Hodges RS, Sykes BD, 1990, Science 249:280-283; Shaw GS et al., 1992a, J Am Chem Soc 114:6258-6259). In addition, an equimolar mixture of SCIII and SCIV has been shown to form preferentially the SCIII/SCIV heterodimer (Shaw GS et al., 1992a, J Am Chem Soc 114:6258-6259). The stabilities of these dimers have been investigated by using 1H-NMR and circular dichroism spectroscopies to follow temperature- and guanidine hydrochloride (GuHCl)-induced denaturations. It has been found that the most stable species, the SCIII/SCIV heterodimer (delta GuH2O = -64.8 kJ/mol), is about 13 kJ/mol more stable than the least stable species, the SCIV homodimer, while the SCIII homodimer is of intermediate stability. This trend of free energies agrees well with the trend of delta G0 values derived from the products of the dissociation constants for calcium binding and peptide association determined from earlier calcium-titration studies. These observations provide evidence that calcium affinity and the association of 2-calcium binding sites are tightly linked. However, it was noted that in all cases delta G0 was considerably more negative than delta GuH2O determined from GuHCl experiments. This difference increased as the stability of the peptide complex increased, providing evidence that linear extrapolation of GuHCl data for very stable proteins may significantly underestimate the value for delta G0.

Thermodynamic properties of the transition state for the rate-limiting step in the folding of the alpha subunit of tryptophan synthase

To gain insight into the physical properties of the transition state for the rate-limiting step in the folding of the alpha subunit of tryptophan synthase from Escherichia coli, the urea dependence of the unfolding reaction was examined as a function of temperature. Consistent with a previous, more limited study [Hurle, M.R., Michelotti, G.A., Crisanti, M.M., & Matthews, C.R. (1987) Proteins 2, 54], the activation entropy for unfolding was found to be negative above 4 M urea. The present study extends this finding to show that both the activation entropy and enthalpy decrease with increasing urea concentrations between 4 and 7.5 M. The change in the heat capacity from the native to the transition state is positive and appears to increase with the denaturant concentration. The urea and temperature dependences of the unfolding rates were analyzed in terms of the denaturant-binding model of Tanford [Tanford, C. (1970) Adv. Protein Chem. 24, 1]. The values for the activation enthalpy and activation entropy of binding are in good agreement with those obtained from a calorimetric study of urea binding to unfolded proteins [Makhatadze, G.I., & Privalov, P.L. (1992) J. Mol. Biol. 226, 491]. These results show that (1) the binding of urea to the transition state of the alpha subunit has thermodynamic properties which are similar to those for urea binding to unfolded proteins, (2) the transition state is distinct from the unfolded conformation and exposes only a fraction of its urea-binding sites to solvent, and (3) the negative value for the activation entropy for unfolding reflects, in part, the ordering of urea on newly exposed surfaces.(ABSTRACT TRUNCATED AT 250 WORDS)

Engineering alternative beta-turn types in staphylococcal nuclease

We have refined the crystal structures of three point mutants of staphylococcal nuclease designed to favor alternative beta-turn types. Single amino acid substitutions were made in a type VIa beta-turn (residues 115-118; Tyr-Lys-Pro-Asn) containing a cis Lys 116-Pro 117 peptide bond. The mutations result in two new backbone conformations, a type I beta-turn for P117T and a type I' beta-turn for P117G and P117A. The P117G and P117A structures exhibit a dramatic difference in backbone conformation in the region of the mutation compared to the nuclease A structure such that the side chain of Lys 116 is reoriented to point into the nucleotide binding pocket. The distinct conformation observed for the nuclease A, P117G, and P117T beta-turn sequences agrees with correlations between beta-turn type and sequence identified from protein crystal structures. The P117A turn conformation provides an exception to these correlations. The results demonstrate that single residue changes can significantly alter backbone conformation, illustrating the process by which diversity in the structure of the protein surface can evolve on a conserved structural core, and suggest protein engineering applications in which the positioning as well as the identify of side chains can be modified to design new enzyme functions. Nuclease variants at the type VIa beta-turn site also allow the relationship between the amino acid sequence and beta-turn conformation to be examined in the context of an identical protein fold in crystallographic detail.

Denaturation behavior of alpha-chymotrypsinogen A in urea and alkylurea solutions: fluorescence studies

The solvent denaturation of alpha-chymotrypsinogen (alpha-ctg A) in aqueous solution of urea, methyl-, N,N'-dimethyl-, ethyl-, propyl- and butylurea was studied by fluorescence measurements. Data were analyzed on the assumption of a two-state approximation to obtain the apparent equilibrium constant, Ku and the apparent Gibbs free energy of transition delta G0u. It has been observed that alkyl-substitution of urea significantly lowers the denaturant concentration needed to denature alpha-ctg A at 25 degrees C. Denaturation was accompanied by the red shift of emission maxima, the increase of the half-width of the fluorescence spectra, the increase of the fluorescence intensity, and the decrease of the fluorescence polarization. The differences of these fluorescence parameters observed for alpha-ctg A in alkylureas and urea can be ascribed to different unfolded states of the protein in different denaturant solutions. Minor differences in the extent of unfolding were confirmed by size-exclusion chromatography.

Correlation of high-temperature stability of alpha-chymotrypsin with 'salting-in' properties of solution

A correlation between the stability of alpha-chymotrypsin against irreversible thermal inactivation at high temperatures (long-term stability) and the coefficient of Setchenov equation as a measure of salting-in/out efficiency of solutes in the Hofmeister series has been found. An increase in the concentration of salting-in solutes (KSCN, urea, guanidinium chloride, formamide) leads to a many-fold decrease of the inactivation rate of the enzyme. In contrast, addition of salting-out solutes has a small effect on the long-term stability of alpha-chymotrypsin at high temperatures. The effects of solutes are additive with respect to their salting-in/out capacities; the stabilizing action of the solutes is determined by the calculated Setchenov coefficient of solution. The correlation is explained by a solute-driven shift of the conformational equilibrium between the 'low-temperature' native and the 'high-temperature' denatured forms of the enzyme within the range of the kinetic scheme put forward in the preceding paper in this journal: irreversible inactivation of the high-temperature form proceeds much more slowly compared with the low-temperature form.

Protein design by binary patterning of polar and nonpolar amino acids

A general strategy is described for the de novo design of proteins. In this strategy the sequence locations of hydrophobic and hydrophilic residues were specified explicitly, but the precise identities of the side chains were not constrained and varied extensively. This strategy was tested by constructing a large collection of synthetic genes whose protein products were designed to fold into four-helix bundle proteins. Each gene encoded a different amino acid sequence, but all sequences shared the same pattern of polar and nonpolar residues. Characterization of the expressed proteins indicated that most of the designed sequences folded into compact alpha-helical structures. Thus, a simple binary code of polar and nonpolar residues arranged in the appropriate order can drive polypeptide chains to collapse into globular alpha-helical folds.

Titin folding energy and elasticity

Molecules of the giant protein titin are responsible for the passive elasticity and central A-band location of muscle myofibrils. The molecular mechanism of titin elasticity is not known, but the I-band region of the molecule appears capable of approximately fourfold reversible extension. Such large extensions are likely to involve unfolding of titin domains. In the present experiments, equilibrium unfolding of titin from rabbit skeletal muscles was studied in vitro by fluorescence and circular dichroism spectroscopy, after addition of guanidinium chloride. The data suggest two unfolding transitions, both of which appear cooperative. The second transition is likely to involve complete unfolding of the immunoglobulin- and fibronectin-like domains from which the molecules is composed. The free energy associated with this transition is comparable with the energy required to extend titin molecules to the maximum amount seen in situ.

Purification and characterization of beta-structural domains of beta-lactoglobulin liberated by limited proteolysis

Incubation of beta-lactoglobulin with immobilized trypsin at 5-10 degrees C results in a time-dependent release of several fragments of the core domain in yields approaching 15%. Digests were fractionated by ion-exchange chromatography with a Mono Q HR 5/5 column and analyzed after disulfide reduction by polyacrylamide gel electrophoresis in sodium dodecylsulfate. Three fragments with approximate molecular weights of 13.8, 9.6, and 6.7 kD were identified. The fraction from ion-exchange chromatography yielding the 6.7 kD fraction after disulfide reduction was further characterized because it was most homogeneous and gave the highest yield. The C-terminal cleavage site of the 6.7 kD core fragment appeared to be Lys100 or Lys101 as determined by C-terminal amino acid analysis. The exact masses, after reduction with dithiothreitol, are 6195 and 6926 as determined by laser desorption mass spectrometry, corresponding to residues 48-101 and 41-100. Prior to reduction, beta-lactoglobulin C-terminal residues 149-162 are connected to these core domain fragments as shown by C-terminal analysis and mass spectrometry. Structural studies indicate that these 7.9 and 8.6 kD core domain fragments released by immobilized trypsin retain much of their native structure. CD spectra indicate the presence of antiparallel beta-sheet structure similar to the native protein but the alpha-helix is lost. Spectra in the aromatic region indicate the existence of tertiary structure. Moreover, structural transitions in urea are completely reversible as measured by CD spectra, although the extrapolated delta GDH20 and the urea concentration at the transition midpoint are lower than for the native protein. The core domain fragments also display a pH-dependent binding to immobilized trans-retinal as does intact protein. A single endotherm is obtained for both core domain fragments and native protein upon differential scanning calorimetry, but again, the domain is less stable as indicated by a transition peak maxima of 56.9 degrees C as compared with 81.1 degrees C for native protein.

Functional methionines in the collagen/gelatin binding domain of plasma fibronectin: effects of chemical modification by chloramine T

Chemical modification of plasma fibronectin (pFn) or its 40-kDa collagen/gelatin binding (CGB) domain by low concentrations of chloramine T (CT), a methionine-specific oxidant, caused decreased binding affinity between pFn or the isolated CGB domain and Sepharose-immobilized denatured collagen or a Texas Red-labeled CNBr fragment CB7 from the alpha 1 chain of type I collagen. Kds obtained by fluid-phase fluorescence polarization binding assays increased upon oxidation about 17-fold for pFn and by 4-fold for the CGB domain. Comparison of CT-oxidized and native CGB domains by endogenous tryptophan fluorescence and CD spectra gave no indication of conformational changes. delta GH2O, the free energy of unfolding at infinite denaturant dilution, derived from guanidinium chloride denaturation curves, differed by less than 0.7 kcal/mol for the oxidized and native CGB domains, indicating essentially equivalent conformational stabilities. We show here that methionyl residues found at positions 412, 432, and 446 are the sites of the oxidative modification. Modification protection experiments carried out in the presence of gelatin demonstrated specific protection of otherwise oxidizable methionyl residues and preservation of high-affinity binding. These results implicate methionyl residues as functional in contributing to high-affinity binding interaction between fibronectin and gelatin.

Dramatic stabilization of ferricytochrome c upon reduction

By combining measurements of the free energy of denaturation of the C102T variant of Saccharomyces cerevisiae iso-1-ferricytochrome c with determination of the formal potentials for the native and chemically-denatured states we have determined the free energy of denaturation of the ferro form of the protein. We report that the simplest of all chemical modifications, addition of an electron, increases the stability of ferricytochrome c by approximately 10 kcal mol-1 at 300 K, pH 4.6. This makes reduced cytochrome c one of the most stable proteins yet investigated.

Partially structured self-associating states of acidic fibroblast growth factor

A combination of near- and far-UV circular dichroism, Fourier-transform infrared spectroscopy, tryptophan fluorescence, size-exclusion chromatography, and a fluorescent extrinsic hydrophobic probe has been employed to characterize partially structured states of human recombinant acidic fibroblast growth factor (aFGF). At low pH, the addition of specific polyanionic ligands or moderate amounts of salts induces states with high secondary but low tertiary structure content. At neutral pH, intermediate amounts of chaotropic agents impose similar partially structured conformational states which also display noncooperative unfolding transitions. Kinetic evidence indicates that similar forms of the protein exist in the first few hundred milliseconds in the refolding pathway of aFGF. The kinetics of their formation appear to be temperature-independent, implying lack of an energy barrier, which is characteristic for further slow folding into the native state. Unlike the native and fully unfolded states, these partially structured conformations exhibit very low solubility, resulting in irreversible aggregation. Potential physiological implications of the existence of such "molten globule" states with regard to the growth factor's transport and biological activity are considered.

Effect of polyanions on the unfolding of acidic fibroblast growth factor

The urea-induced unfolding of acidic fibroblast growth factor (aFGF) in the presence and absence of various polyanions has been quantitatively examined by fluorescence spectroscopy. In the absence of a stabilizing polyanion, the apparent free energy of unfolding of aFGF is 6.5 kcal mol-1. The presence of equimolar or greater amounts of heparin stabilizes aFGF from unfolding by more than 2.5 kcal mol-1 and slows the rate of unfolding by greater than 2000-fold. The ability of heparin to stabilize aFGF is critically dependent upon many factors including the number of aFGF molecules bound to the heparin chain, ionic strength, temperature, and the extent of sulfation of the polysaccharide. The presence of similar amounts of other polyanions such as sulfated beta-cyclodextrin or heparan sulfate also stabilizes aFGF to a similar extent as heparin. Additional experiments demonstrate that increasing charge density enhances the ability of polyanions such as sulfated beta-cyclodextrins, phosphorylated inositols, and modified heparins to protect aFGF from urea-induced unfolding.

Molecular dynamics study of the stability of staphylococcal nuclease mutants: component analysis of the free energy difference of denaturation

The stability of two mutants G88V (Gly-88-->Val) and A69T (Ala-69-->Thr) of staphylococcal nuclease was analyzed by molecular dynamics simulations. The calculated free energy differences of denaturation for G88V and A69T were -1.1 and -2.8 kcal/mol, respectively. These values are in good agreement with the experimental values. The free energy differences divided into electrostatic and van der Waals components were analyzed. These two mutants are mainly destabilized due to van der Waals interactions. There is little difference between the electrostatic contribution to the free energy change in the native state and that in the denatured state. In each mutant structure, a small cavity appears in the vicinity of the perturbed residue. It is suggested that intramolecular van der Waals interactions of the mutants are weaker than those of the wild-type. Furthermore, analyses of the contributions of each residue near the perturbed residue and of water to the free energy difference of denaturation suggest that the interaction between water and the perturbed residue plays a very important role in the stability of staphylococcal nuclease, and that a small hydrophobic core consisting of the three aromatic rings (Tyr-27, Phe-34, Phe-76) and the side chain of Met-32 is also important for the stability.

The energetics and cooperativity of protein folding: a simple experimental analysis based upon the solvation of internal residues

The reversible unfolding of two dissimilar proteins, phosphoglycerate kinase from Bacillus stearothermophilus (PGK) and Staphylococcus aureus nuclease (SAN), was induced with two denaturants, urea and guanidinium chloride (GuHCl). For each protein, structural transitions were monitored by intrinsic fluorescence intensity changes arising from a unique tryptophan residue. In the case of SAN the single, native tryptophan residue was used, whereas for PGK two versions, one with a tryptophan at position 315 and one at 379, were constructed genetically. The resultant folding curves were analyzed by considering the change in the solvation free energy of internal amino acid residues as the denaturant concentration was varied. We derive the following simple relationship: -RT ln K = delta Gw + n delta Gs,m[D]/Kden. + [D]) where K is the equilibrium constant describing the distribution of folded and unfolded forms at a given denaturant concentration [D], delta Gw is the free energy change for the transition in the absence of denaturant, and n is the number of internal side chains becoming exposed. delta Gs,m and Kden. are constants derived empirically from the solvation energies of model compounds and represent the behavior of an average internal side chain between 0 and 6 M GuHCl and 0 and 8 M urea. For proteins of known structure these values can easily be derived, and for others, average values in guanidinium chloride (delta Gs,m = 0.775 kcal/mol and Kden. = 5.4 M) or urea (delta Gs,m = 1.198 kcal/mol and Kden. = 25.25 M) can be used in the analysis. Results show that the parameters n and delta Gw are independent of the denaturant used for all 12 transitions studied. This supports the hypothesis that the unfolding activity of urea and GuHCl can be accounted for by their effect on the solvation energy of amino acid side chains which are buried in the folded but exposed in the unfolded protein. This simple analytical treatment allows the "cooperativity" of protein folding to be interpreted in terms of the number of side chains becoming exposed to the solvent in a given step and allows accurate estimation of the free energy irrespective of the denaturant concentration needed to induce the transition.