Stable intermediates can be trapped during the reversible refolding of urea-denatured rhodanese

Glycation induced conformational transitions in cystatin proceed to form biotoxic aggregates: A multidimensional analysis

Hyperglycaemic conditions facilitate the glycation of serum proteins which may have predisposition to aggregation and thus lead to complications. The current study investigates the glycation induced structural and functional modifications of chickpea cystatin (CPC) as well as biological toxicity of the modified protein forms, using CPC-glucose as a model system. Several structural intermediates were formed during the incubation of CPC with glucose (day 4, 8, 12, & 16) as revealed by circular dichroism (CD), altered intrinsic fluorescence, and high ANS binding. Further incubation of CPC with glucose (day 21) formed abundant β structures as revealed by Fourier transform infrared spectroscopy and CD analysis which may be due to the aggregation of protein. High thioflavin T fluorescence intensity and increased Congo red absorbance together with enhanced turbidity and Rayleigh scattering by this modified form confirmed the aggregation. Electron microscopy finally provided the valid physical authentication about the presence of aggregate structures. Functional inactivation of glucose incubated CPC was also observed with time. Single cell electrophoresis of lymphocytes and plasmid nicking assays in the presence of modified CPC showed the DNA damage which confirmed its biological toxicity. Hence, our study suggests that glycation of CPC not only leads to structural and functional alterations in proteins but also to biotoxic AGEs and aggregates.

Glycation promotes the formation of genotoxic aggregates in glucose oxidase

This study investigates the effect of pentose sugars (ribose and arabinose) on the structural and chemical modifications in glucose oxidase (GOD) as well as genotoxic potential of this modified form. An intermediate state of GOD was observed on day 12 of incubation having CD minima peaks at 222 and 208 nm, characteristic of α-helix and a few tertiary contacts with altered tryptophan environment and high ANS binding. All these features indicate the existence of molten globule state of the GOD with ribose and arabinose on day 12. GOD on day 15 of incubation forms β structures as revealed by CD and FTIR which may be due to its aggregation. Furthermore, GOD on day 15 showed a remarkable increase in Thioflavin T fluorescence at 485 nm. Comet assay of lymphocytes and plasmid nicking assay in presence of glycated GOD show DNA damage which confirmed the genotoxicity of advance glycated end products. Hence, our study suggests that glycated GOD results in the formation of aggregates and the advanced glycated end products, which are genotoxic in nature.

The aggregation state of rhodanese during folding influences the ability of GroEL to assist reactivation

The in vitro folding of rhodanese involves a competition between formation of properly folded enzyme and off-pathway inactive species. Co-solvents like glycerol or low temperature, e.g. refolding at 10 degrees C, successfully retard the off-pathway formation of large inactive aggregates, but the process does not yield 100% active enzyme. These data suggest that mis-folded species are formed from early folding intermediates. GroEL can capture early folding intermediates, and it loses the ability to capture and reactivate rhodanese if the enzyme is allowed first to spontaneously fold for longer times before it is presented to GroEL, a process that leads to the formation of unproductive intermediates. In addition, GroEL cannot reverse large aggregates once they are formed, but it could capture some folding intermediates and activate them, even though they are not capable of forming active enzyme if left to spontaneous refolding. The interaction between GroEL and rhodanese substantially but not completely inhibits intra-protein inactivation, which is responsible for incomplete activation during unassisted refolding. Thus, GroEL not only decreases aggregation, but it gives the highest reactivation of any method of assistance. The results are interpreted using a previously suggested model based on studies of the spontaneous folding of rhodanese (Gorovits, B. M., McGee, W. A., and Horowitz, P. M. (1998) Biochim. Biophys. Acta 1382, 120--128 and Panda, M., Gorovits, B. M., and Horowitz, P. M. (2000) J. Biol. Chem. 275, 63--70).

Productive and nonproductive intermediates in the folding of denatured rhodanese

The competition between protein aggregation and folding has been investigated using rhodanese (thiosulfate:cyanide sulfurtransferase, EC 2.8.1.1) as a model. During folding from a urea-denatured state, rhodanese rapidly forms associated species or intermediates, some of which are large and/or sticky. The early removal of such particles by filtration results in a decreased refolding yield. With time, a portion of the smaller aggregates can partition back first to intermediates and then to refolded protein, while a fraction of these irreversibly form unproductive higher aggregates. Dynamic light scattering measurements indicate that the average sizes of the aggregates formed during rhodanese folding increase from 225 to 325 nm over 45 min and they become increasingly heterogeneous. Glycerol addition or the application of high hydrostatic pressure improved the final refolding yields by stabilizing smaller particles. Although addition of glycerol into the refolding mixture blocks the formation of unproductive aggregates, it cannot dissociate them back to productive intermediates. The presence of 3.9 M urea keeps the aggregates small, and they can be dissociated to monomers by high hydrostatic pressure even after 1 h of incubation. These studies suggest that early associated intermediates formed during folding can be reversed to give active species.

High hydrostatic pressure can reverse aggregation of protein folding intermediates and facilitate acquisition of native structure

The present work demonstrates that high hydrostatic pressure can increase protein folding by reducing nonspecific aggregation. Protein aggregation is one of the main side reactions that competes with protein folding, and it typically results from interactions among partially folded intermediates. It is known that oligomeric proteins can be dissociated by the application of high hydrostatic pressure. Since protein aggregates can be described as nonspecific protein oligomers, it can be predicted that they can be completely or partially dissociated by pressure. The enzyme rhodanese is prone to slow aggregation in 3.9 M urea, and it is widely used as a model for the folding of a protein which readily aggregates. In the present study, it was demonstrated that this aggregation process could be completely reversed under high hydrostatic pressure. Release of the pressure led to renewed protein aggregation. In addition, it was demonstrated that refolding of urea-denatured rhodanese at 2 kbar pressure led to an increased yield of the native enzyme. The final recovery was increased up to approximately 25% in contrast to approximately 5% recovery observed under ambient pressure. The recovery can be further increased in the presence of 4 M glycerol, where 56% of the protein was recovered by treatment with high pressure. These observations suggest that some protein aggregation can be limited without the use of chemical additives, and they show that the pressures needed to maintain solubility are considerably less than those typically required for dissociation of specific oligomers and unfolding of polypeptide chains.

Rhodanese folding is controlled by the partitioning of its folding intermediates

Rhodanese is used widely as a model for protein folding, since the enzyme as usually studied refolds poorly unless the process is assisted. Here, the influence of the partitioning of the folding intermediates of bovine rhodanese on the efficiency of its refolding has been investigated. Metastable intermediates can be formed during unfolding of the enzyme. The stabilities of these intermediates and the native protein with respect to chemical unfolding can be greatly increased by high concentrations of glycerol. The concentration dependence of the protein folding kinetics indicates that associative processes occur during renaturation. It is suggested that, during enzyme refolding, rhodanese undergoes fast collapse to an intermediate state I' which partitions to at least two other states (I" and I"'). One of these states (I"') is able to refold to the native enzyme, while the other state (I") is in equilibrium with I' and is prone to slow irreversible aggregation. Stabilization of I" against irreversible aggregation by glycerol results in increased yield of the protein refolding and a complex temperature dependence of the protein renaturation. The nature of the I" type intermediate has been investigated. Based on the fact that extensive hydrophobic surfaces are exposed during formation of the intermediates, it is suggested that partial dissociation of the two structural domains of rhodanese is an early event in unfolding. Interactions of different folding intermediates of rhodanese with the chaperonin GroEL were investigated, and the results suggest that the more extensively unfolded intermediates bind tighter than those that appear later on the rhodanese refolding pathway.

ATP hydrolysis is critical for induction of conformational changes in GroEL that expose hydrophobic surfaces

The degree of hydrophobic exposure in the molecular chaperone GroEL during its cycle of ATP hydrolysis was analyzed using 1,1'-bis(4-anilino)naphthalene-5,5'disulfonic acid (bisANS), a hydrophobic probe, whose fluorescence is highly sensitive to the environment. In the presence of 10 mM MgCl2 and 10 mM KCl the addition of ATP, but not ADP or AMP-PNP, resulted in a time-dependent, linear increase in the bisANS fluorescence. The rate of the increase in the bisANS fluorescence depended on the concentrations of both GroEL and the probe. The effect could be substantially inhibited by addition of excess ADP or by converting ATP to ADP using hexokinase, showing that the increase in the bisANS fluorescence was correlated with ATP hydrolysis. The rate of ATP hydrolysis catalyzed by GroEL was uncompetitively inhibited in the presence of bisANS. This uncompetitive inhibition suggests that the probe can interact with the GroEL-ATP complex. The inability of the nonhydrolyzable ATP analog, AMP-PNP, to cause a similar effect is explained by the interaction of bisANS with a transient conformational state of GroEL formed consequent to ATP hydrolysis. It is suggested that this short lived hydrophobic exposure reflects a conformational shift in GroEL that results from electrostatic repulsion between the bound products of ATP hydrolysis, and it plays an important role in the mechanism of the chaperonin cycle.

Protein folding in the central cavity of the GroEL-GroES chaperonin complex

The chaperonin GroEL is able to mediate protein folding in its central cavity. GroEL-bound dihydrofolate reductase assumes its native conformation when the GroES cofactor caps one end of the GroEL cylinder, thereby discharging the unfolded polypeptide into an enclosed cage. Folded dihydrofolate reductase emerges upon ATP-dependent GroES release. Other proteins, such as rhodanese, may leave GroEL after having attained a conformation that is committed to fold. Incompletely folded polypeptide rebinds to GroEL, resulting in structural rearrangement for another folding trial in the chaperonin cavity.

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.

Secretion of both partially unfolded and folded apoproteins of dimethyl sulfoxide reductase by spheroplasts from a molybdenum cofactor-deficient mutant of Rhodobacter sphaeroides f. sp. denitrificans

Spheroplasts prepared from a molybdenum cofactor-deficient mutant of Rhodobacter sphaeroides f. sp. denitrificans secreted dimethyl sulfoxide (DMSO) reductase which had no molybdenum cofactor and therefore no activity, whereas those from wild-type cells secreted the active reductase. The inactive DMSO reductase proteins were separated by nondenaturing electrophoresis into two forms: form I, with the same mobility as the native enzyme, and form II, with slower mobility. Both forms had the same mobility on denaturing gel. Form I and active DMSO reductase had the same profile on gel filtration chromatography. Form II was eluted a little faster than the native enzyme, suggesting that DMSO reductase form II was not an aggregated form but a compactly folded form very similar to the native enzyme. Form II was digested by trypsin and denatured with urea, whereas form I was unaffected, like native DMSO reductase. These results suggested that form II was a partially unfolded but compactly folded apoprotein of DMSO reductase.

Physical characterization of a reactivatable liposome-bound rhodanese folding intermediate

Recently, we described the formation of a complex between liposomes and the unfolded protein rhodanese (thiosulfate:cyanide sulfurtransferase, EC 2.8.1.1), which could be liberated and efficiently reactivated after treatment of the complex with detergents [Zardeneta, G., & Horowitz, P. M. (1992) Eur. J. Biochem. 210, 831-837]. Previous data suggested that liposome-bound rhodanese was in the form of a folding intermediate. We have characterized in greater detail the nature of the conformation of the bound rhodanese. Physical characterization of the bound rhodanese intermediate was carried out using proteolysis, fluorescence studies with 1,8-anilinonapthalene-8-sulfonic acid, a probe for hydrophobic site exposure, intrinsic fluorescence to determine tryptophan accessibility using the quenchers acrylamide and iodide, and circular dichroism to detect extent of secondary structure. These studies show that the rhodanese intermediates bound to either cardiolipin or phosphatidylserine liposomes are not identical, the former being in a less compact conformation yet having more secondary structure than the latter, an observation which may explain why the reactivation of the former intermediate is more effective. Finally, turbidimetric and proteolytic studies raise the possibility that each rhodanese intermediate binds to several liposomes. This finding suggests that a possible reason for the differential reactivation yields obtained may be due to the fact that unfolded rhodanese has more binding sites for cardiolipin than for phosphatidylserine liposomes. A greater number of binding sites would result in better anchoring of rhodanese's interactive surfaces and thus reduce the likelihood of misfolding.

Inactivation precedes conformation change during thermal denaturation of adenylate kinase

During the thermal denaturation of rabbit muscle adenylate kinase, the extents and rates of both unfolding and aggregation are dependent on protein concentration. Under identical conditions, inactivation takes place at a lower temperature than noticeable conformational changes and aggregation as measured by fluorescence, second derivative absorption spectroscopy, far ultraviolet circular dichroism and light scattering. Kinetics of inactivation can be resolved into two phases and at the same protein concentrations, the unfolding and aggregation rates are about one order of magnitude slower than the fast phase and approximately the same as the slow phase rate of the inactivation reaction between 35 and 60 degrees C. This is in general accord with the suggestion made previously that the active site of this enzyme is situated in a region more flexible than the molecule as a whole (Tsou, C.L. (1986) Trends Biochem. Sci. 11, 427-429). The inactivated enzyme cannot be reactivated by cooling and standing at 4 degrees C but can be over 80% reactivated by cooling and first standing in 3 M guanidine hydrochloride followed by diluting out the denaturant.

Inactivation before significant conformational change during denaturation of papain by guanidine hydrochloride

During denaturation by GuHCl, papain shows a rapid decrease in activity with increasing concentrations of the denaturant followed by an intermediate stage of relatively little change from 1 to 2 M before complete inactivation at 4 M GuHCl. At GuHCl concentrations lower than 2 M, enzyme activity is more sensitive to GuHCl than noticeable conformation changes as followed by fluorescence and CD measurements. Kinetics of GuHCl inactivation were studied by following the substrate reaction in the presence of denaturant and the apparent rate constants thus obtained were found to be only slightly higher than those for conformational changes. However, apparent inactivation rate constants obtained in the presence of saturating concentration of substrate are actually inactivation constants for the ES complex. The inactivation rates at different substrate concentrations were, therefore, followed and the microscopic inactivation rate constants for the free enzyme obtained (Tsou, C.L. (1988) Adv. Enzymol. 61, 381-436). It was found that substrate protects strongly against inactivation and at the same GuHCl concentration, the inactivation rate of the free enzyme is 100-fold higher than that of unfolding. The above results show that the activity of papain is more sensitive to GuHCl than its overall conformation and like the enzymes previously studied in this laboratory, its active site is more flexible than the enzyme molecule as a whole.

Thermally perturbed rhodanese can be protected from inactivation by self-association

A fluorescence-detected structural transition occurs in the enzyme rhodanese between 30-40 degrees C that leads to inactivation and aggregation, which anomalously decrease with increasing protein concentration. Rhodanese at 8 micrograms/ml is inactivated at 40 degrees C after 50 min of incubation, but it is protected as its concentration is raised, such that above 200 micrograms/ml, there is only slight inactivation for at least 70 min. Inactivation is increased by lauryl maltoside, or by low concentrations of 2-mercaptoethanol. The enzyme is protected by high concentrations of 2-mercaptoethanol or by the substrate, thiosulfate. The fluorescence of 1,8-anilinonaphthalene sulfonate reports the appearance of hydrophobic sites between 30-40 degrees C. Light scattering kinetics at 40 degrees C shows three phases: an initial lag, a relatively rapid increase, and then a more gradual increase. The light scattering decreases under several conditions; at increased protein concentration; at high concentrations of 2-mercaptoethanol; with lauryl maltoside; or with thiosulfate. Aggregated enzyme is inactive, although enzyme can inactivate without significant aggregation. Glutaraldehyde cross-linking shows that rhodanese can form dimers, and that higher molecular weight species are formed at 40 degrees C but not at 23 degrees C. Precipitates formed at 40 degrees C contain monomers with disulfide bonds, dimers, and multimers. We propose that thermally perturbed rhodanese has increased hydrophobic exposure, and it can either: (a) aggregate after a rate-limiting inactivation; or (b) reversibly dimerize and protect itself from inactivation and the formation of large aggregates.

GroEL and GroES increase the specific enzymatic activity of newly-synthesized rhodanese if present during in vitro transcription/translation

Enzymatically active mammalian rhodanese, a mitochondrial matrix enzyme, which has been found to require assistants for efficient refolding in vitro, has been synthesized from a plasmid in a cell-free, fractionated, coupled transcription/translation system derived from Escherichia coli. The bacterial chaperonins, GroEL and GroES, along with the rhodanese substrate thiosulfate greatly enhance the specific enzymatic activity of the rhodanese polypeptide that is formed. Indirect evidence suggests that the effect of the GroEL/ES chaperonins is on ribosome-bound nascent peptides. The in vitro transcription/translation system produces sufficient amounts of rhodanese to provide a system for studying factors that control the initial steps in folding of nascent proteins.

A chaperone-mimetic effect of serum albumin on rhodanese

Reactivation of denatured rhodanese (thiosulfate:cyanide sulfurtransferase, EC 2.8.1.1) was found to be aided by the presence of serum albumin. Both the rate and the extent of reactivation of the urea-denatured enzyme were optimal at low rhodanese and moderate serum albumin concentrations. Similarly, stabilization of the sulfurtransferase activity of rhodanese that had been partially unfolded at 40 degrees C was aided by the presence of serum albumin. All the observations are in accord with a model in which enzyme that has been partially refolded from the urea-denatured state or partially unfolded thermally interacts directly with serum albumin in a way that prevents rhodanese self-association. Serum albumin thus acts as a molecular chaperone in these systems.

Recombinant bovine rhodanese: purification and comparison with bovine liver rhodanese

Recombinant bovine rhodanese (thiosulfate: cyanide sulfurtransferase, EC 2.8.1.1) has been purified to homogeneity from Escherichia coli BL21(DE3) by cation-exchange chromatography. Recombinant and bovine liver rhodanese coelectrophorese under denaturing conditions, with an apparent subunit molecular weight of 33,000. The amino terminal seven residues of the recombinant protein are identical to those of the bovine enzyme, indicating that E. coli also removes the N-terminal methionine. The Km for thiosulfate is the same for the two proteins. The specific activity of the recombinant enzyme is 12% higher (816 IU/mg) than that of the bovine enzyme (730 IU/mg). The two proteins are indistinguishable as to their ultraviolet absorbance and their intrinsic fluorescence. The ability of the two proteins to refold from 8 M urea to enzymatically active species was similar both for unassisted refolding, and when folding was assisted either by the detergent, lauryl maltoside or by the E. coli chaperonin system composed of cpn60 and cpn10. Bovine rhodanese is known to have multiple electrophoretic forms under native conditions. In contrast, the recombinant protein has only one form, which comigrates with the least negatively charged of the bovine liver isoforms. This is consistent with the retention of the carboxy terminal residues in the recombinant protein that are frequently removed from the bovine liver protein.

Purification of bovine liver rhodanese by low-pH column chromatography

We report a purification of bovine liver rhodanese (thiosulfate:cyanide sulfurtransferase, EC 2.8.1.1) using column chromatography under conditions that take advantage of recent information regarding the structure and stability of this enzyme. At low pH (e.g., pH 4-6), rhodanese is stabilized against inactivation processes. By maintaining rhodanese at low pH, column chromatography, and especially ion-exchange chromatography, becomes practical, without loss of enzymatic activity. A purification method involving the sequential use of cation-exchange, size-exclusion, and hydrophobic-interaction chromatography was developed, and rhodanese was purified with good yield to electrophoretic purity and high specific activity. Previous methods for purifying bovine liver rhodanese employ repeated ammonium sulfate fractionations and crystallization of the rhodanese. In these methods, it is difficult to separate rhodanese from yellow-brown contaminants in the final stages of the procedures. Here, yellow-brown contaminants, which copurify with rhodanese on the first two columns, are completely resolved by hydrophobic interaction chromatography. This method can be readily scaled up, requires no special equipment, eliminates the variability inherent in previous methods, and is less dependent upon experience.