Proline peptide isomerization and the reactivation of denatured enzymes

Mutation in the interdomain tether influences the stability and refolding of the enzyme rhodanese

Rhodanese is a single polypeptide chain of 293 amino acids that is folded into two globular domains of nearly equal size that are connected by a 16 amino acid tether. Two amino acids, Val-Asp (VD), were inserted into the interdomain tether through site-directed mutagenesis to produce the new interdomain sequence, E145PSRPEPAIFKAVDTLNR. The purified mutant protein, when unperturbed, was virtually indistiguishable in all properties tested and gave a specific activity that was at least 90% of the WT. However, the tether mutant was considerably less stable to perturbation compared with the WT enzyme. The interdomain hydrophobic surfaces in the mutant were more easily exposed, and the formation of intermediate folding states was facilitated. The rate of unassisted refolding was slightly less for the mutant, and the yield of active enzyme was somewhat reduced. The mutation introduced a new V8 proteinase cleavage site, but this site was not accessible in the native mutant which was as resistant to proteolysis as the WT enzyme. However, perturbation with low concentrations of urea that could form folding intermediate(s), allowed facile cleavage of the mutant to give fragments that appeared to represent the individual domains. In addition, the perturbed mutant could be proteolyzed close to one end of the polypeptide, a position that is far from the site of mutation, and which was not readily cleaved in the WT enzyme or the native form of the mutant. These results indicate that mutation in the interdomain tether can have dramatic effects on the stability and conformational transitions of rhodanese.

The kinetic studies on the intramolecular SH, S-S exchange reaction of bovine mercaptalbumin

Bovine mercaptalbumin (BMA) has 17 disulfide bonds and one SH group at Cys-34 which catalyzes the intramolecular SH, S-S exchange reaction (N-A isomerization, molecular aging) in the alkaline region at low ionic strength, resulting in the formation of the aged form (A-form). The aging reaction was completely reversible and strongly affected by environmental factors, such as pH, temperature, ionic strength, Ca2+, nonbranched short-chain fatty acids, etc. Disulfide configuration (or pairing of disulfide bonds) was affected by the environmental factors. Obtained results might support the concept of Klotz (1966) that protein conformation (or three-dimensional structure) is dependent upon (i) the primary structure and (ii) constituents of the solvent.

Human immunodeficiency viral protease is catalytically active as a fusion protein: characterization of the fusion and native enzymes produced in Escherichia coli

Processing of the gag and pol gene precursor proteins of retroviruses is essential for the production of mature infectious virions. The processing is directed by a viral protease that itself is part of these precursors and is presumed to cleave itself autocatalytically. To facilitate study of this process, the protease was produced as a fusion protein in Escherichia coli. In this construct, the 10,793-Da protease was preceeded by two copies of a modified IgG binding domain derived from protein A. The IgG binding domain was linked to the protease by an Asp-Pro peptide bond which could not be cleaved by the viral protease. A dimer of the 25,400-Da fusion protein was catalytically active, specifically cleaving a substrate peptide at the correct Tyr-Pro bond. Thus, the fusion protein could serve as a model of the viral gag-pol polyprotein. The finding that the fusion protein was catalytically active supports the suggestion that a gag-pol dimer can initiate a proteolytic cascade after budding of the immature virus. The fusion protein also provided a source of authentic protease. The protease was released from the fusion construct by incubation with formic acid, cleaving the Asp-Pro linkage which had been inserted between the IgG binding domain and the protease.

A physical characterization of sulfane sulfurtransferase

The bacterial enzyme sulfane sulfurtransferase has been studied using spectroscopic techniques. The enzyme was characterized in terms of its near-UV absorption spectrum, molar ellipticity, intrinsic fluorescence spectra and the effects of general and ionic quenching reagents upon its fluorescence. Fluorescence model studies are consistent with sulfane sulfurtransferase having only a single tryptophan residue, which accounts for its low UV absorption coefficient and suggested that this residue is at least partially exposed to solvent. Second derivative absorption spectroscopy studies revealed that most of the bacterial enzyme's tyrosine residues are exposed to solvent. Unlike the better known sulfurtransferase, bovine liver rhodanese, sulfane sulfurtransferase does not undergo a detectable increase in quantum yield when shifting from the sulfur-containing covalent enzyme intermediate to the free enzyme form (which lacks sulfur) during catalysis. CD studies suggest that sulfane sulfurtransferase has a significantly higher proportion of alpha-helix than rhodanese. The renaturation of sulfane sulfurtransferase denatured in 6 M guanidine was shown to be rapid and complete provided that the enzyme had not been oxidized while in the denatured state. Sulfane sulfurtransferase, like rhodanese, catalyzes the transfer of sulfur from thiosulfate to cyanide via a persulfide intermediate, and displays remarkably similar kinetics in this process (Aird, B.A., Heinrikson, R.L. and Westley, J. (1987) J. Biol. Chem 262, 17327-17335). In light of this, the results of the structural studies with sulfane sulfurtransferase are compared and contrasted to data from similar experiments with rhodanese in hopes that they would provide insight about which phenomena observed with rhodanese are intrinsic to the process of transferring sulfur atoms.

The effects of lauryl maltoside on the reactivation of several enzymes after treatment with guanidinium chloride

The present study confirms the previous reports that detergents can facilitate the reactivation of guanidinium chloride (GdmCl) denatured rhodanese (Tandon, S. and Horowitz, P. (1986) J. Biol. Chem. 261, 15615-15618; Tandon, S. and Horowitz, P. (1987) J. Biol. Chem. 262, 4486-4491). Here, we report the effect of the detergent, lauryl maltoside, on the reactivation of several enzymes other than rhodanese. For this study we used five different enzymes each having a single polypeptide chain, namely: adenosine deaminase; 3-phosphoglyceric phosphokinase; myokinase; 3 alpha-hydroxysteroid dehydrogenase; and phosphoglucomutase. The regain of enzyme activity was used to monitor refolding. Like rhodanese, these enzymes were denatured in 6 M GdmCl and diluted into a buffer containing various concentrations of lauryl maltoside. The effect of lauryl maltoside on reactivating these proteins depended on the specific enzyme used. For example, in the presence of lauryl maltoside, reactivation of adenosine deaminase increased to 98%, while phosphoglucomutase could not be reactivated significantly. The critical micelle concentration (CMC) of lauryl maltoside was measured under the present experimental conditions using 2-(p-toluidinyl)naphthalene 6-sulfonate (TNS) as an apolar fluorescent probe, and gave a value of 0.085 mg.ml-1 in 10 mM sodium phosphate (pH 7.4). The reactivating effect of lauryl maltoside was not generally related to its CMC. In some cases an induction period was observed before the enzyme attained its steady-state velocity. This might suggest the presence of intermediate(s) in the refolding pathway that could have been stabilized by the detergent. These findings indicate that 'non-denaturing' detergents may be useful for assisting reactivation of enzymes, although the optimum conditions will have to be determined for each individual case.

The rate of equine liver alcohol dehydrogenase denaturation by urea. Dependence on temperature and denaturant concentration

The kinetics of the irreversible urea denaturation of equine liver alcohol dehydrogenase have been studied as a function of temperature and urea concentration. The unfolding of the macromolecule, monitored by means of the phosphorescence properties of a deeply buried tryptophan residue, was found to be strictly a two-state process over the entire temperature range. It is characterized by a steep dependence on urea concentration typical of highly cooperative transitions and below room temperature it possesses large negative activation energies. The reaction is comparatively slow, does not seem to be preceded by a fast phase, and the rate-limiting step does not have the characteristics of proline isomerization. When the data are analyzed in terms of binding equilibria the temperature dependence results from an anomalously large change in heat capacity. Although this is a property of strong hydrophobic interactions in model compounds the slow rates of denaturation are best understood with a model of protein stability which emphasizes the cooperative nature of intramolecular interactions such as hydrogen bonding.

Folding of homologous proteins. The refolding of different ribonucleases is independent of sequence variations, proline content and glycosylation

The refolding kinetics of four different pancreatic ribonucleases have been compared. Bovine and ovine RNAase contain 4 proline residues, red deer RNAase has 5 prolines, the enzyme from roe deer 6 prolines. Despite the variation in the amount of prolines, all four proteins show a constant value of 20% fast refolding species UF. The extra proline residues of the deer enzymes do not increase the amount of slow refolding species US. Consequently these residues may be non-essential for folding. Despite many differences in the amino acid sequence, the rates if the fast and slow refolding reactions are very similar for all investigated ribonucleases. This indicates that the pathway of refolding has been conserved during evolution, i.e. the positions where amino acid substitutions occur are not critically important for the rate-determining steps of the folding process. A carbohydrate chain attached to ribonuclease does not alter the folding properties of the protein: RNAase A and RNAase B from roe deer show identical refolding kinetics.

Physicochemical characterization of a fast refolding monomeric class I fructose-1,6-bisphosphate aldolase from Staphylococcus aureus

The class I fructose-1,6-bisphosphate aldolase from Staphylococcus aureus is proposed as a good candidate for thermodynamic and kinetic studies on protein folding. The monomeric enzyme (molecular weight 35 000 +/- 1000) has been previously described as 'unusually heat-stable' [F. Götz et al. (1980) Eur. J. Biochem. 108, 295-301]. In the present paper we show that the enzyme is reversibly denatured at relatively low temperature (26-39 degrees C), as determined by protein fluorescence and far ultraviolet circular dichroism; the van't Hoff enthalpy of the thermal unfolding is 355 +/- 63 kJ/mol. The dichroic absorption shows that the aldolase is extensively unfolded in 6 M guanidine/HCl. Complete reactivation of the guanidine-denatured enzyme in the test solution is extremely fast (less than 10 s in the temperature range from 24.6 degrees C to 7.7 degrees C). Reactivation ought to be much slower if isomerization reactions around at least some of the ten Xaa-Pro peptide bonds were rate-limiting for reactivation.

Structural intermediates in folding of yeast iso-2 cytochrome c

The kinetic properties of the folding reactions of iso-2 cytochrome c from Saccharomyces cerevisiae have been investigated by stopped-flow and temperature-jump methods. Three different structural probes are compared: (1) absorbance changes in the visible reflecting changes in heme environment, (2) ultraviolet absorbance changes due to the exposure of aromatic groups to solvent, and (3) tryptophan fluorescence attributable principally to the average distance between the tryptophan residue (donor) and the heme (quencher). In addition, two probes either indicative of or correlated with function, ascorbic acid reducibility and the 695-nm absorbance band, have been used to monitor specifically the rate of formation of the native protein on refolding. The fastest phase observed (tau 3) has a measurable relative amplitude only when monitored by visible absorbance changes, suggesting that this reaction involves changes in heme environment in the absence of significant changes in the heme to tryptophan distance or in the extent to which aromatic groups are exposed to solvent. Different slow phases are observed when complete refolding is monitored by visible or ultraviolet absorbance (tau 1a) as opposed to tryptophan fluorescence (tau 1b), the fluorescence changes being complete on a time scale 4-8-fold faster than for absorbance. A mid-range kinetic phase (tau 2) is detected by all three structural probes. When ascorbic acid reducibility or 695-nm absorbance changes are used to monitor the rate of formation of the native protein, two phases are detected: tau 2 and tau 1a. Taken together these results demonstrate that kinetic phase tau 1b results in the formation of a structural intermediate in folding with fluorescence close to that of the native protein but with distinct absorbance properties.

Trimeric intermediate in the in vivo folding and subunit assembly of the tail spike endorhamnosidase of bacteriophage P22

Newly synthesized tail spike polypeptide chains mature from trypsin- and NaDodSO4-sensitive unfolded chains to trypsin- and NaDodSO4-resistant native trimers with a t1/2 of 5 min at 30 degrees C. A metastable intermediate in subunit folding and assembly was trapped by chilling and isolated by electrophoresis through nondenaturing gels in the cold. A fraction of the intermediate could be matured into native trimers in vitro by incubating at physiological temperature. Mixing experiments with electrophoretically distinct mutant proteins showed that the precursor that matured in vitro represented three tail spike polypeptide chains already associated with each other but not fully folded. Identification of this intermediate reveals that the processes of polypeptide chain folding and subunit assembly are coupled in this large structural protein.

Identification and characterization of the direct folding process of hen egg-white lysozyme

Refolding kinetics of hen egg-white lysozyme (HEWL) have been studied by means of the stopped-flow method with guanidinium chloride as the denaturant. We show here that the three-species model U1 in equilibrium or formed from U2 in equilibrium or formed from N (U1 and U2 = unfolded; N = native) now established for pancreatic ribonuclease A is also valid for HEWL on the basis of the following lines of evidence: (1) refolding kinetics outside the transition region are biphasic; (2) dependence of the fractional amplitude for the fast phase on the ratio of the time constants of the two phases agrees with theory; (3) unfolding kinetics outside the transition region are of single phase; (4) direct evidence for the U2 leads to U1 transformation is obtained by double-jump experiments; (5) the time constant of the binding reaction of a substrate analogue, 4-methylumbelliferyl N,-N'-diacetyl-beta-chitobioside, to HEWL molecules during refolding reaction agrees with the time constant of the direct refolding phase U2 leads to N. The characteristic properties of the nucleation-controlled reaction of refolding of small globular proteins are discussed in general. The results of the discussion are used to suggest that the direct folding process is nucleation controlled from the experimental results of the temperature dependence of the refolding rate.

Nature of the fast and slow refolding reactions of iron(III) cytochrome c

The fast and slow refolding reactions of iron(III) cytochrome c (Fe(III) cyt c), previously studied by Ikai et al. (Ikai, A., Fish, W. W., & Tanford, C. (1973) J. Mol. Biol. 73, 165--184), have been reinvestigated. The fast reaction has the major amplitude (78%) and is 100-fold faster than the slow reaction in these conditions (pH 7.2, 25 degrees C, 1.75 M guanidine hydrochloride). We show here that native cyt c is the product formed in the fast reaction as well as in the slow reaction. Two probes have been used to test for formation of native cyt c. absorbance in the 695-nm band and rate of reduction of by L-ascorbate. Different unfolded species (UF, US) give rise to the fast and slow refolding reactions, as shown both by refolding assays at different times after unfolding ("double-jump" experiments) and by the formation of native cyt c in each of the fast and slow refolding reactions. Thus the fast refolding reaction is UF leads to N and the slow refolding reaction is Us leads to N, where N is native cyt c, and there is a US in equilibrium UF equilibrium in unfolded cyt c. The results are consistent with the UF in equilibrium US reaction being proline isomerization, but this has not yet been tested in detail. Folding intermediates have been detected in both reactions. In the UF leads to N reaction, the Soret absorbance change precedes the recovery of the native 695-nm band spectrum, showing that Soret absorbance monitors the formation of a folding intermediate. In the US leads to N reaction an ascorbate-reducible intermediate has been found at an early stage in folding and the Soret absorbance change occurs together with the change at 695 nm as N is formed in the final stage of folding.

Stepwise cleavage of the pro part of promelittin by dipeptidylpeptidase IV. Evidence for a new type of precursor--product conversion

Melittin, the main constituent of honeybee venom, is derived from promelittin. In the amino acid sequence of the 'pro' region of this precursor, every second residue is either proline or alanine. The possibility has been investigated that activation of promellitin might proceed via sequential liberation of dipeptides catalyzed by a dipeptidylpeptidase IV. As substrates we used promelittin isolated from queen bees fed with radioactive proline, and enzymatic fragments of prepromelittin which contained the entire pro part and the NH2-terminal hexapeptide of melittin. It could first be demonstrated that pig kidney of dipeptidyleptides catalyzed by a dipeptidylpeptidase IV. As substrates we used promelittin isolated from queen bees fed with radioactive proline, and enzymatic fragments of prepromelittin which contained the entire pro part and the NH2-terminal hexapeptide of melittin. It could first be demonstrated that pig kidney of dipeptidylpeptidase IV releases dipeptides from the pro part. An enzyme of this type could then be detected in extracts from venom glands of q bees, which also contain a dipeptidase. After inhibiting the latter enzyme with mersalyl, a stepwise cleavage of dipeptides, starting at the amino end of the pro region could be demonstrated. This hydrolysis did not proceed into the melittin sequence. Furthermore, fragments with an extra residue at the amino end, which therefore had the wrong 'reading frame' for the dipeptidylpeptidase, were not hydrolyzed. With intact promelittin as substrate the rate of hydrolysis was always lower than with the fragments. The results presented in this paper suggest a new type of precursor-product conversion proceeding via stepwise cleavage of dipeptide units. Our experimental evidence also ascribes a biological function to a dipeptidylpeptidase IV, a type of enzyme widely distributed in animals tissues. The evidence, that the observed reaction in vitro reflects the mechanism of promelittin activation in vivo is discussed.