Interactive intermediates are formed during the urea unfolding of rhodanese

Apolipoprotein E4 exhibits intermediates with domain interaction

ApoE4(C112R) is the strongest risk factor for Alzheimer's disease, while apoE3(C112) is considered normal. The C112R substitution is believed to alter the interactions between the N-terminal (NTD) and the C-terminal domain (CTD) leading to major functional differences. Here we investigate how the molecular property of the residue at position 112 affects domain interaction using an array of C112X substitutions with arginine, alanine, threonine, valine, leucine and isoleucine as 'X'. We attempt to determine the free energy of domain interaction (∆G_INT) from stabilities of the NTD (∆G_NTD) and CTD (∆G_CTD) in the full-length apoE, and the stabilities of fragments of the NTD (∆G_NTF) and CTD (∆G_CTF), using the relationship, ∆G_INT = ∆G_NTD + ∆G_CTD - ∆G_NTF - ∆G_CTF. We find that although ∆G_NTD is strongly dependent on the C112X substitutions, ∆G_NTD - ∆G_NTF is small. Furthermore, ∆G_CTD remains nearly the same as ∆G_CTF. Therefore, ∆G_INT is estimated to be small and similar for the apoE isoforms. However, stability of domain interaction monitored by urea dependent changes in interdomain Forster Resonance Energy Transfer (FRET) is found to be strongly dependent on C112X substitutions. ApoE4 exhibits the highest mid-point of denaturation of interdomain FRET. To resolve the apparently contradictory observations, we hypothesize that higher interdomain FRET in apoE4 in urea may involve 'intermediate' states. Enhanced fluorescence of bis-ANS and susceptibility to proteolytic cleavage support that apoE4, specifically, the NTD of apoE4 harbor 'intermediates' in both native and mildly denaturing conditions. The intermediates could hold key to the pathological functions of apoE4.

Conformational analysis of champedak galactose-binding lectin under different urea concentrations

Conformational analysis of champedak galactose-binding (CGB) lectin under different urea concentrations was studied in phosphate-buffered saline (pH 7.2) using far-ultraviolet circular dichroism (far-UV CD), tryptophan (Trp) fluorescence and ANS fluorescence. In all cases, CGB lectin displayed a two-step, three-state transition. The first transition (from the native state to the intermediate state) started at ∼2.0 M urea and ended at ∼4.5 M urea, while the second transition (from the intermediate state to the completely denatured state) was characterized by the start- and end-points at ∼5.75 M and ∼7.5 M urea, respectively, when analyzed by the emission maximum of Trp fluorescence. A marked increase in the Trp fluorescence, ANS fluorescence and -CD values at 218 nm (-CD218 nm) represented the first transition, whereas a decrease in these parameters defined the second transition. On the other hand, emission maximum of the Trp fluorescence showed a continuous increase throughout the urea concentration range. Transformation of tetramer into monomer represented the first transition, whereas the second transition reflected the unfolding of monomer. Far-UV CD, Trp fluorescence and ANS fluorescence spectra were used to characterize the native, the intermediate and the completely denatured states of CGB lectin, obtained at 0.0 M, 5.0 M and 9.0 M urea, respectively. The intermediate state was characterized by the presence of higher secondary structures, increased ANS binding as well as increased Trp fluorescence intensity. A gradual decrease in the hemagglutination activity of CGB lectin was observed with increasing urea concentrations, showing complete loss at 4.0 M urea.

Stretched extracellular matrix proteins turn fouling and are functionally rescued by the chaperones albumin and casein

While evidence is mounting that cells exploit protein unfolding for mechanochemical signal conversion (mechanotransduction), what mechanisms are in place to deal with the unwanted consequences of exposing hydrophobic residues upon force-induced protein unfolding? Here, we show that mechanical chaperones exist that can transiently bind to hydrophobic residues that are freshly exposed by mechanical force. The stretch-upregulated binding of albumin or casein to fibronectin fibers is reversible and does not inhibit fiber contraction once the tension is released.

GAPDH is conformationally and functionally altered in association with oxidative stress in mouse models of amyotrophic lateral sclerosis

It is proposed that conformational changes induced in proteins by oxidation can lead to loss of activity or protein aggregation through exposure of hydrophobic residues and alteration in surface hydrophobicity. Because increased oxidative stress and protein aggregation are consistently observed in amyotrophic lateral sclerosis (ALS), we used a 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (BisANS) photolabeling approach to monitor changes in protein unfolding in vivo in skeletal muscle proteins in ALS mice. We find two major proteins, creatine kinase (CK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), conformationally affected in the ALS G93A mouse model concordant with a 43% and 41% reduction in enzyme activity, respectively. This correlated with changes in conformation and activity that were detected in CK and GAPDH with in vitro oxidation. Interestingly, we found that GAPDH, but not CK, is conformationally and functionally affected in a longer-lived ALS model (H46R/H48Q), exhibiting a 22% reduction in enzyme activity. We proposed a reaction mechanism for BisANS with nucleophilic amino acids such as lysine, serine, threonine, and tyrosine, and BisANS was found to be primarily incorporated to lysine residues in GAPDH. We identified the specific BisANS incorporation sites on GAPDH in nontransgenic (NTg), G93A, and H46R/H48Q mice using liquid chromatography-tandem mass spectrometry analysis. Four BisANS-containing sites (K52, K104, K212, and K248) were found in NTg GAPDH, while three out of four of these sites were lost in either G93A or H46R/H48Q GAPDH. Conversely, eight new sites (K2, K63, K69, K114, K183, K251, S330, and K331) were found on GAPDH for G93A, including one common site (K114) for H46R/H48Q, which is not found on GAPDH from NTg mice. These data show that GAPDH is differentially affected structurally and functionally in vivo in accordance with the degree of oxidative stress associated with these two models of ALS.

A Novel Approach for Screening the Proteome for Changes in Protein Conformation

Changes in surface hydrophobicity are generally considered as a sensitive indicator for monitoring the structural alterations of proteins that are often associated with changes in function. Currently, no technique has been developed to screen a complex mixture of proteins for changes in the conformation of specific proteins. In this study, we adapted a UV photolabeling approach, using an apolar fluorescent probe, 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (BisANS), to monitor changes in surface hydrophobic domains in either purified rhodanese or skeletal muscle cytosolic proteins by urea-induced unfolding or in response to in vitro metal-catalyzed oxidation. Using two-dimensional polyacrylamide gel electrophoresis (2D PAGE), we identified two specific proteins in skeletal muscle cytosol that exhibited a marked loss of incorporation of BisANS after exposure to in vitro oxidative stress: creatine kinase (CK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We found that the activities of both enzymes were also reduced significantly in response to oxidative stress. We then determined if this method could detect changes in surface hydrophobicity in specific proteins arising from oxidative stress generated in vivo by muscle denervation. A loss in surface hydrophobic domains in CK and GAPDH was again observed as measured by the BisANS photoincorporation approach. In addition, the CK and GAPDH activity in denervated muscle was markedly reduced. These data demonstrate for the first time that this assay can screen a complex mixture of proteins for alterations in surface hydrophobic domains of individual proteins.

The role of detergent in refolding of GdnHCl-denatured arginine kinase from shrimpFenneropenaeus Chinensis: the solubilization of aggregate and refolding in detergent solutions

Strong aggregation occurred in the refolding route of arginine kinase (AK) denatured with 3 mol GdnHCl/L (GdnHCl, guanidine hydrochloride). The activity recovery of GdnHCl-denatured AK was very low and dependent on the protein concentration in the process of refolding. For denatured AK at 1.2 µmol/L concentration, the recovered activity yield was about 45.2% of the native enzyme, whereas at 5.2 µmol/L the activity recovery yield was only 20% of native activity. The nonionic detergent Triton X-100 and Tween 20 (≤100 mmol/L concentration) not only effectively blocked the aggregation but also enabled the denatured AK to recover most of its native activity. The kinetics of aggregate solubilization showed that there was an induction phase dependent on the detergent, but there was no dependency when detergent was absent. The apparent activity recovery had a cooperative relation with detergents in the process of refolding, which suggested the existence of some interaction between the detergent and the refolding intermediate. On the basis of the study results, a scheme of refolding was proposed.Key words: arginine kinase, guanidine-denatured, refolding, detergent, aggregation.

Folding intermediates of the prion protein stabilized by hydrostatic pressure and low temperature

Prion diseases are associated with conformational conversion of the cellular prion protein, PrPC, into a misfolded form, PrPSc. We have investigated the equilibrium unfolding of the structured domain of recombinant murine prion protein, comprising residues 121-231 (mPrP-(121-231)). The equilibrium unfolding of mPrP-(121-231) by urea monitored by intrinsic fluorescence and circular dichroism (CD) spectroscopies indicated a two-state transition, without detectable folding intermediates. The fluorescent probe 4,4'-dianilino-1,1'-binaphthyl-5,5-disulfonic acid (bis-ANS) binds to native mPrP-(121-231), indicating exposure of hydrophobic domains on the protein surface. Increasing concentrations of urea (up to 4 M) caused the release of bound bis-ANS, whereas changes in intrinsic fluorescence and CD of mPrP took place only above 4 M urea. This indicates the existence of a partially unfolded conformation of mPrP, characterized by loss of bis-ANS binding and preservation of the overall structure of the protein, stabilized at low concentrations of urea. Hydrostatic pressure and low temperatures were also used to stabilize partially folded intermediates that are not detectable in the presence of chemical denaturants. Compression of mPrP to 3.5 kbar at 25 degrees C and pH 7 caused a slight decrease in intrinsic fluorescence emission and an 8-fold increase in bis-ANS fluorescence. Lowering the temperature to -9 degrees C under pressure reversed the decrease in intrinsic fluorescence and caused a marked (approximately 40-fold) increase in bis-ANS fluorescence. The increase in bis-ANS fluorescence at low temperatures was similar to that observed for mPrP at 1 atm at pH 4. These results suggest that pressure-assisted cold denaturation of mPrP stabilizes a partially folded intermediate that is qualitatively similar to the state obtained at acidic pH. Compression of mPrP in the presence of a subdenaturing concentration of urea stabilized another partially folded intermediate, and cold denaturation under these conditions led to complete unfolding of the protein. Possible implications of the existence of such partially folded intermediates in the folding of the prion protein and in the conversion to the PrPSc conformer are discussed.

Rhodanese can partially refold in its GroEL-GroES-ADP complex and can be released to give a homogeneous product

Molecular chaperones GroEL and GroES facilitate reactivation of denatured rhodanese which folds poorly unless the process is assisted. The present work tests the hypothesis that more extensively unfolded forms of rhodanese bind tighter than those forms that appear later in the folding pathway. The study of the interaction of different urea-induced forms of rhodanese with GroEL suggests that species preceding the domain folded form bind directly and productively to GroEL. Rhodanese partially folds while in the GroEL-GroES-ADP complex, but it does not significantly reach an active state. Partially folded rhodanese can be released from the GroEL-GroES-ADP complex by subdenaturing concentrations of urea as a homogeneous species that is committed to fold to the native conformation with little or no partitioning to the aggregated state. Dilution of denatured rhodanese to the same final concentration gives less active enzyme and significant aggregation. Urea denaturation studies show that active rhodanese released from complexes behaves identically to native enzyme, while spontaneously folded rhodanese has a different stability. These results are interpreted using a previously proposed model based on studies of unassisted rhodanese folding [Gorovits, B. M., McGee, W. A., and Horowitz, P. M. (1998) Biochim. Biophys. Acta 1382, 120-128. Panda, M., Gorovits, B. M., and Horowitz, P. M. (2000) J. Biol. Chem. 275, 63-70].

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).

The structural differences between bovine lens alphaA- and alphaB-crystallin

Lens alphaA- and alphaB-crystallin have been reported to act differently in their protection against nonthermal destabilization of proteins. The nature of this difference, however, is not completely understood. Therefore we used a combination of thermally and solvent-induced structural changes to investigate the difference in the secondary, tertiary and quaternary structures of alphaA- and alphaB-crystallin. We demonstrate the relationship between the changes in the tertiary and quaternary structures for both polypeptides. Far-ultraviolet circular dichroism revealed that the secondary structure of alphaB-crystallin is more stable than that of alphaA-crystallin, and the temperature-induced secondary structure changes of both polypeptides are partially reversible. Tryptophan fluorescence revealed two distinct transitions for both alphaA- and alphaB-crystallin. Compared to alphaB-crystallin, both transitions of alphaA-crystallin occurred at higher temperature. The changes in the hydrophobicity are accompanied by changes in the quaternary structure and are biphasic, as shown by bis-1-anilino-8-naphthalenesulfonate fluorescence and sedimentation velocity. These phenomena explain the difference in the chaperone capacity of alphaA- and alphaB-crystallin carried out at different temperatures. The quaternary structure of alpha-crystallin is more stable than that of alphaA- and alphaB-crystallin. The latter has a strong tendency to dissociate under thermal or solvent destabilization. This phenomenon is related to the difference in subunit organization of alphaA- and alphaB-crystallin where both hydrophobic and ionic interactions are involved. We find that an important subunit rearrangement of alphaA-crystallin takes place once the molecule is destabilized. This subunit rearrangement is a requisite phenomenon for maintaining alpha-crystallin in its globular form and as a stable complex. On the base of our results, we suggest a four-state model describing the folding and dissociation of alphaA- and alphaB-crystallin better than a three-state model [Sun et al. (1999) J. Biol. Chem. 274, 34067-34071].

Aggregation, dissociation and unfolding of glucose dehydrogenase during urea denaturation

The effect of urea on glucose dehydrogenase from Bacillus megaterium has been studied by following changes in enzymatic activity, conformation and state of aggregation. It was found that the denaturation process involves several transitions. At very low urea concentrations (below 0.5 M), where the enzyme is fully active and tetrameric, there is a conformational change as monitored by an increase in intensity of the tryptophan fluorescence and a maximum exposure of organized hydrophobic surfaces as reported by the fluorescence of 4,4'-dianilino-1,1'-binaphthyl-5.5'-disulfonic acid. At slightly higher urea concentrations (0.75-2 M), a major conformational transition occurs, as monitored by circular dichroism and fluorescence measurements, in which the enzyme activity is completely lost and is concomitant with the formation of interacting intermediates that lead to a highly aggregated state. Increasing urea concentrations cause a complete dissociation to lead first a partially and eventually the complete unfolded monomer. These phenomena are fully reversible by dilution of denaturant. It is concluded that after urea denaturation, the folding/assembly pathway of glucose dehydrogenase occurs with the formation of intermediate species in which transient higher aggregates appear to be involved.

Alteration around the active site of rhodanese during urea-induced denaturation and its implications for folding

The enzyme rhodanese contains two globular domains connected by a tether region and associated by strong hydrophobic interactions. The protein has proven to be very difficult to refold without assistance to prevent oxidation and aggregation. For this study, the active site cysteine 247, near the interdomain region, was modified with the environmentally sensitive fluorescent probe, 2-(4'-(iodoacetamido)anilino)naphthalene-6-sulfonic acid (IAANS), to yield a derivative that reversibly unfolds. Structural transitions during urea unfolding/refolding were complex and multiphasic. Increasing urea concentrations increased the IAANS fluorescence intensity and polarization. Both values reached maxima at approximately 4 m urea, where there is a concomitant large exposure of hydrophobic sites as reported by both IAANS and the noncovalent fluorescent probe, bis-ANS. The exposure of the hydrophobic sites arises from the decrease in strong interaction between the domain interfaces, which lead to their partial separation. This correlates with the loss of activity of the unlabeled enzyme. Above 4.5 m urea, there is progressive loss of rigid, hydrophobic surfaces, and both fluorescence and polarization of IAANS decrease, with accompanying loss of secondary structure. These results are consistent with a folding model in which there is an initial, rapid hydrophobic collapse of the denatured form to an intermediate with native like secondary structure, with exposed interdomain, hydrophobic surfaces. This step is followed by adjustment of the domain-domain interactions and the proper positioning of reduced cysteine 247 at the active site.

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.

Domain separation precedes global unfolding of rhodanese

The enzyme rhodanese was investigated for the conformational transition associated with its urea unfolding. When rhodanese was treated with 0 or 3 M urea, the activity was not significantly affected. 4.25 M urea treatment led to a time-dependent loss of activity in 60 min. Rhodanese was completely inactivated within 2 min in 6 M urea. The 1,1'-bi(4-anilino)naphthalene-5,5'-disulfonic acid fluorescence intensity was not significantly increased during 0, 3, and 6 M urea equilibrations, and the fluorescence was dramatically increased with 4.25 M urea, indicating that hydrophobic surfaces are exposed. After 0 and 3 M urea equilibration, rhodanese was not significantly proteolyzed with trypsin. Treatment with 4.25 M urea led to simultaneous formation of major 12-, 15.9-, 17-, and 21.2-kDa fragments, followed by progressive emergence of smaller peptides. The N termini of the 17- and 21.2-kDa bands were those of intact rhodanese. The N terminus of the 15.9-kDa band starts at the end of the interdomain tether. The 12-kDa band begins with either residue 183 or residue 187. The size and sequence information suggest that the 17- and 15.9-kDa bands correspond to the two domains. The 21.2- and 12-kDa bands appear to be generated through one-site tryptic cleavage. It is concluded that urea disrupts interaction between the two domains, increasing the accessibility of the interdomain tether that can be digested by trypsin. The released domains have increased proteolytic susceptibility and produce smaller peptides, which may represent subdomains of rhodanese.

Alkali metal ions protect mitochondrial rhodanese against thermal inactivation

Incubation of bovine liver mitochondrial rhodanese in dilute, reducing solutions at temperatures ranging between 30 and 45 degreesC conduced to a rapid loss of enzymatic activity. This inactivation was substantially reduced in the presence of millimolar concentrations of alkali metal ions, divalent cations (including Mg2+, Ca2+, and Ba2+) were ineffective. The extent of protection afforded by monovalent cations was highly dependent on their ionic radii, with K+ and Na+ ions being the most effective protective agents. The protection afforded by a number of anions, including thiosulfate, could be totally ascribed to the presence of the accompanying monovalent cation. The overall results indicate that K+ and Na+, at concentrations and temperatures within the physiological range, substantially contribute to the stabilization of the functional structure of rhodanese.

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.

Covalent reinforcement of a fragile region in the dimeric enzyme thymidylate synthase stabilizes the protein against chaotrope-induced unfolding

Urea and guanidinium chloride induced unfolding of thymidylate synthase, a dimeric enzyme, and engineered interface mutants have been monitored by circular dichroism, fluorescence, and size-exclusion chromatography. Equilibrium unfolding studies show biphasic transitions, with a plateau between 3.5 and 5 M urea, when monitored by far-UV CD and fluorescence energy transfer employing an (aminoethylamino) naphthalenesulfonyl (AEDANS) label at the active site residue, Cys198. AEDANS was also specifically incorporated at position Cys155 in the mutant protein T155C. Direct excitation of this extrinsic fluorophore in the wild type protein (labeled at Cys198) and mutant T155C (labeled at Cys155) showed remarkable differences in the unfolding profiles. C155 AEDANS has a transition centered at 3.5 M urea, which is in contrast to Cys 198 AEDANS (5.5 M urea). Unfolding studies monitored by following intrinsic fluorescence of Trp residues which are located in a small structural domain suggest that this region of the protein is intrinsically fragile. The stable equilibrium intermediate is identified to be an ensemble of partially unfolded aggregated species by gel filtration studies. The chaotrope-induced denaturation of TS appears to proceed through a partially unfolded intermediate that is stabilized by aggregation. Dissociation and loss of structure occur concomitantly at high denaturant concentrations. Introduction of two symmetrically positioned disulfide bridges across the dimer interface in the triple mutant T155C/E188C/C244T (TSMox) stabilized the protein against denaturant-induced unfolding. Aggregate formation was completely abolished in the mutant TSMox, which also enhanced the overall structural stability of the protein. Structural reinforcement of the fragile interface in thymidylate synthase results in dramatic stabilization toward chaotrope-induced unfolding.

Covalent tethering of the dimer interface annuls aggregation in thymidylate synthase

Thymidylate synthase (TS), a dimeric enzyme, forms large soluble aggregates at concentrations of urea (3.3-5M), well below that required for complete denaturation, as established by fluorescence and size-exclusion chromatography. In contrast to the wild-type enzyme, an engineered mutant of TS (T155C/E188C/C244T), TSMox, in which two subunits are crosslinked by disulfide bridges between residues 155-188' and 188-155' does not show this behavior. Aggregation behavior is restored upon disulfide bond reduction in the mutant protein, indicating the involvement of interface segments in forming soluble associated species. Intermolecular disulfide crosslinking has been used as a probe to investigate the formation of larger non-native aggregates. The studies argue for the formation of large multimeric species via a sticky patch of polypeptide from the dimer interface region that becomes exposed on partial unfolding. Covalent reinforcement of relatively fragile protein-protein interfaces may be a useful strategy in minimizing aggregation of non-native structures in multimeric proteins.

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.

Subunit dissociation and unfolding of macrophage NO synthase: relationship between enzyme structure, prosthetic group binding, and catalytic function

Macrophage NO synthase is a homodimer of 130 kDa subunits. Each subunit contains an oxygenase domain that binds iron protoporphyrin IX (heme) and tetrahydrobiopterin (H4biopterin) and a reductase domain that binds FAD, FMN, and calmodulin (CaM) [Ghosh & Stuehr (1995) Biochemistry 34, 801-807]. We have studied the dissociation and unfolding reactions of dimeric iNOS in urea to learn how enzyme structure relates to catalysis and prosthetic group binding. The iNOS dimer dissociated between 0 and 2.5 M urea, and the subunits partially unfolded at 2.5 M urea and above. Dimer dissociation was accompanied by loss of NO synthesis activity and release of bound H4biopterin from the protein. However, the dissociated subunits maintained their cytochrome c and ferricyanide reductase activities and retained near stoichiometric quantities of bound heme. The subunit unfolding transition was accompanied by loss of reductase activities and partial loss of bound heme but retention of bound flavins and CaM. The heme iron in the dissociated subunits remained coordinated through axial cysteine thiolate ligation. Kinetic analysis of dimer dissociation showed that loss of NO synthesis correlated with a loss of heme Soret absorbance at 398 nm and an appearance of absorbance bands at 377 and 460 nm, which were attributed to DTT coordination to the sixth position of the heme iron to form a mixed bisthiolate complex. Subunits could reassociate into a dimer when incubated with L-arginine and H4biopterin. Dimer formation correlated with proportional recoveries of NO synthesis and heme Soret absorbance at 398 nm. Thus, dimeric iNOS undergoes separate dissociation and unfolding transitions in urea, and each transition is accompanied by a loss of a specific catalytic function.(ABSTRACT TRUNCATED AT 250 WORDS)

Rhodanese conformational changes permit oxidation to give disulfides that form in a kinetically determined sequence

When the structure of the monomeric enzyme rhodanese is perturbed by urea or SDS and heat, sulfhydryl assays combined with SDS gel analyses reveal that intrachain disulfides are formed rapidly. Two intrachain disulfide bonded species can be distinguished. One contains a single disulfide and comigrates on SDS gels with fully reduced rhodanese (Band I), while a second species contains two disulfides and migrates faster than the reduced enzyme (Band II). The kinetic path and identity of the participating sulfhydryl groups are suggested by the results with sulfhydryl mutants. On mild oxidation or perturbation, a single disulfide forms that involves two of the three sulfhydryl groups in C-terminal domain of the protein, i.e., two of the sulfhydryl groups from among the three residues: the active-site Cys-247, Cys-254 and Cys-263. These disulfides are the same as those that are formed upon oxidation of the native enzyme. The remaining sulfhydryl group of these three, in a kinetically slower process, can form a disulfide with Cys-63 which is in the N-terminal domain in native rhodanese. The resulting looped structure is so conformationally constrained that its shape and/or altered SDS binding gives rise to the 'fast' Band II on the SDS gels. The conformationally constrained species with two disulfides may be related to oxidized rhodanese species that are difficult to reduce.

Folding and aggregation of TEM beta-lactamase: analogies with the formation of inclusion bodies in Escherichia coli

The enzyme TEM beta-lactamase has been used as a model for understanding the pathway leading to formation of inclusion bodies in Escherichia coli. The equilibrium denaturation of TEM beta-lactamase revealed that an intermediate that has lost enzymatic activity, native protein fluorescence, and UV absorption, but retains 60% of the native circular dichroism signal, becomes populated at intermediate (1.0-1.4 M) concentrations of guanidium chloride (GdmCl). This species exhibits a large increase in bis-1-anilino-8-naphthalene sulfonic acid fluorescence, indicating the presence of exposed hydrophobic surfaces. When TEM beta-lactamase was unfolded in different initial concentrations of GdmCl and refolded to the same final conditions by dialysis a distinct minimum in the yield of active protein was observed for initial concentrations of GdmCl in the 1.0-1.5 M range. It was shown that the lower reactivation yield was solely due to the formation of noncovalently linked aggregates. We propose that the aggregation of TEM beta-lactamase involves the association of a compact state having partially exposed hydrophobic surfaces. This hypothesis is consistent with our recent findings that TEM beta-lactamase inclusion bodies contains extensive secondary structure (Przybycien TM, Dunn JP, Valax P, Georgiou G, 1994, Protein Eng 7:131-136). Finally, we have also shown that protein aggregation was enhanced at higher temperatures and in the presence of 5 mM dithiothreitol and was inhibited by the addition of sucrose. These conditions exert a similar effect on the formation of inclusion bodies in vivo.