Urea-induced Unfolding Transitions Research Articles

Stable monomers in the ancestral sequence reconstruction of the last opisthokont common ancestor of dimeric triosephosphate isomerase.

Function and structure are strongly coupled in obligated oligomers such as Triosephosphate isomerase (TIM). In animals and fungi, TIM monomers are inactive and unstable. Previously, we used ancestral sequence reconstruction to study TIM evolution and found that before these lineages diverged, the last opisthokonta common ancestor of TIM (LOCATIM) was an obligated oligomer that resembles those of extant TIMs. Notably, calorimetric evidence indicated that ancestral TIM monomers are more structured than extant ones. To further increase confidence about the function, structure, and stability of the LOCATIM, in this work, we applied two different inference methodologies and the worst plausible case scenario for both of them, to infer four sequences of this ancestor and test the robustness of their physicochemical properties. The extensive biophysical characterization of the four reconstructed sequences of LOCATIM showed very similar hydrodynamic and spectroscopic properties, as well as ligand-binding energetics and catalytic parameters. Their 3D structures were also conserved. Although differences were observed in melting temperature, all LOCATIMs showed reversible urea-induced unfolding transitions, and for those that reached equilibrium, high conformational stability was estimated (ΔGTot = 40.6-46.2 kcal/mol). The stability of the inactive monomeric intermediates was also high (ΔGunf = 12.6-18.4 kcal/mol), resembling some protozoan TIMs rather than the unstable monomer observed in extant opisthokonts. A comparative analysis of the 3D structure of ancestral and extant TIMs shows a correlation between the higher stability of the ancestral monomers with the presence of several hydrogen bonds located in the "bottom" part of the barrel.

Analysis of the pH-dependent thermodynamic stability, local motions, and microsecond folding kinetics of carbonmonoxycytochrome c

This paper analyzes the effect of pH on thermodynamic stability, low-frequency local motions and microsecond folding kinetics of carbonmonoxycytochrome c (Cyt-CO) all across the alkaline pH-unfolding transition of protein. Thermodynamic analysis of urea-induced unfolding transitions of Cyt-CO measured between pH 6 and pH 11.9 reveals that Cyt-CO is maximally stable at pH∼9.5. Dilution of unfolded Cyt-CO into refolding medium forms a native-like compact state (NCO-state), where Fe2+−CO interaction persists. Kinetic and thermodynamic parameters measured for slow thermally-driven CO dissociation (NCO→N+CO) and association (N+CO→NCO) reactions between pH 6.5 and pH 13 reveal that the thermal-motions of M80-containing Ω-loop are decreased in subdenaturing limit of alkaline pH. Laser photolysis of Fe2+-CO bond in NCO-state triggers the microsecond folding (NCO→N). The microsecond kinetics measured all across the alkaline pH-unfolding transition of Cyt-CO produce rate rollover in the refolding limb of chevron plot, which suggests a glass transition of NCO en route to N. Between pH 7 and pH 11.9, the natural logarithm of the microsecond folding rate varies by < 1.5 units while the natural logarithm of apparent equilibrium constant varies by 11.8 units. This finding indicates that the pH-dependent ionic-interactions greatly affect the global stability of protein but have very small effect on folding kinetics.

Urea Interactions with Native and Unfolded Proteins: A Volumetric Study

We describe a statistical thermodynamics-based approach to analyzing urea-dependent volumetric properties of proteins. The analysis produces the thermodynamic properties of elementary reactions in which a urea molecule interacts with a protein while also yielding an estimate of the effective solvent-accessible surface areas of the native and unfolded protein states. We carried out high precision measurements of the partial molar volume and adiabatic compressibility of lysozyme, apocytochrome c, ribonuclease A, and α-chymotrypsinogen A at 25°C as a function of urea. The resulting volumetric data were analyzed within the framework of a statistical thermodynamic formalism. Lysozyme remains folded, while apocytochrome c is unfolded between 0 and 8 M urea. In contrast, ribonuclease A and α-chymotrypsinogen A exhibit urea-induced unfolding transitions. Thus, our data permit us to characterize urea-protein interactions in both the native and unfolded states. We interpreted the urea-dependent volumetric properties of urea in terms of equilibrium constant, k, and changes in volume, ΔV0, and compressibility, ΔKT0, for an elementary reaction of urea binding to protein with a concomitant release of two water molecules from its hydration shell. Comparison of the values of k, ΔV0, and ΔKT0 with the similar data obtained for small molecules mimicking protein groups reveals the lack of cooperative effects involved in urea-protein interactions. Urea-dependent volumetric data enable one to evaluate the extent of solvent exposure of protein groups in both the native and unfolded states. We emphasize that the volumetric approach offers a practical way for evaluating the effective solvent accessible surface area of biologically significant fully or partially unfolded polypeptides.

A Reason for Long Tales

Transcription Activator-Like Effectors (TALEs) are bacterial virulence factors containing a domain of repeats that recognize specific DNA sequences and reprogram transcription activation of invaded plant cells. TALE genes encode 5 to 30 repeats with average pairwise repeat identities greater than 91%. Most variability arises from only two positions termed Repeat Variable Diresidues (RVDs), which confer DNA binding specificity. Crystal structures of free and DNA-bound TALEs (Deng et al. Science 2012) show a large conformational change upon DNA binding. Thus, DNA binding is likely coupled to the free energy of tertiary structural change between the TALE repeats. We are interested in quantifying this relationship and relating it to folding cooperativity using nearest-neighbor (“Ising”) models.To investigate the length dependence of folding, we created a set of consensus TALE constructs of varying length. Solubilizing N- and C-terminal caps are needed to favor monomeric protein in solution as detected by sedimentation velocity analytical ultracentrifugation. Capped consensus TALE repeat constructs have alpha-helical secondary structure as measured by farUV CD. Urea-induced unfolding transitions of TALE repeat arrays were measured and show cooperative unfolding transitions as well as increases in stability with length. These data are well-fitted by an Ising model, which separates the contributions of intrinsic and interfacial free energies. TALE repeats have an unfavorable intrinsic folding free energy of 5.3 kcal/mol and a favorable interfacial free energy of −6.8 kcal/mol. Using these values, the length dependence of TALE stability can be modeled, and shows TALEs under 5 repeats to be unfolded. Using the Ising parameters, we find that partially folded states with a single repeat unfolded are energetically accessible. Population of these partially folded states may be important for DNA binding.

Interactions of urea with native and unfolded proteins: a volumetric study.

We describe a statistical thermodynamic approach to analyzing urea-dependent volumetric properties of proteins. We use this approach to analyze our urea-dependent data on the partial molar volume and adiabatic compressibility of lysozyme, apocytochrome c, ribonuclease A, and α-chymotrypsinogen A. The analysis produces the thermodynamic properties of elementary urea-protein association reactions while also yielding estimates of the effective solvent-accessible surface areas of the native and unfolded protein states. Lysozyme and apocytochrome c do not undergo urea-induced transitions. The former remains folded, while the latter is unfolded between 0 and 8 M urea. In contrast, ribonuclease A and α-chymotrypsinogen A exhibit urea-induced unfolding transitions. Thus, our data permit us to characterize urea-protein interactions in both the native and unfolded states. We interpreted the urea-dependent volumetric properties of the proteins in terms of the equilibrium constant, k, and changes in volume, ΔV0, and compressibility, ΔKT0, for a reaction in which urea binds to a protein with a concomitant release of two waters of hydration to the bulk. Comparison of the values of k, ΔV0, and ΔKT0 with the similar data obtained on small molecules mimicking protein groups reveals lack of cooperative effects involved in urea-protein interactions. In general, the volumetric approach, while providing a unique characterization of cosolvent-protein interactions, offers a practical way for evaluating the effective solvent accessible surface area of biologically significant fully or partially unfolded polypeptides.

Microsecond Folding Dynamics of Apomyoglobin at Acidic pH

Apomyolgobin (apoMb) is an important model for understanding the folding mechanism of helical proteins. This study focuses on a partially structured state of sperm whale apoMb populated at pH 4.2 (M-state), which structurally resembles a late kinetic intermediate in the formation of the native state (N) at higher pH. The thermodynamics and cooperativity of apoMb folding at pH 4.2 and 6.2 were studied by global analysis of the urea-induced unfolding transitions monitored by tryptophan fluorescence and circular dichroism. The kinetics of folding and unfolding of apoMb at pH 4.2 was measured over a time window from 40 to 850 μs, using fluorescence-detected continuous-flow measurements. Our observation of biphasic kinetics provides clear evidence for rapid (<100 μs) accumulation of previously unresolved intermediate states in both refolding and unfolding experiments. Quantitative kinetic modeling of the results, using a four-state mechanism with two intermediates on a direct route between the unfolded and folded states (U↔I↔L↔M), gave new insight into the conformational states and barriers that precede the rate-limiting step in the formation of the N-state of apoMb.

Local and Coupled Thermodynamic Stability of the Two-Domain and Bifunctional Enzyme SlyD from Escherichia coli

SlyD (sensitive to lysis D) is a protein folding helper enzyme comprising peptidylprolyl isomerase as well as chaperone activities at the respective FKBP and IF domains. Both domains coact concerning the peptidylprolyl isomerase activity on protein substrates. Using various biophysical techniques and NMR spectroscopy, the local and global thermodynamic stability of the variant (1-165) of SlyD from Escherichia coli (SlyD*) was characterized. Structurally, both domains are rather independent. The urea-induced unfolding transitions of the two domain protein monitored by 2D NMR spectroscopy and amide proton exchange experiments, however, showed that the IF domain experiences a reduced local stability under both native and unfolding conditions compared to the FKBP domain. Nevertheless, the entire protein shows highly cooperative unfolding at elevated denaturing conditions. This cooperativity is significantly reduced in a SlyD* variant missing the IF domain. The quite low local stability due to high internal fluctuations of the IF domain might be the prerequisite for the ubiquitous chaperone function of SlyD. One physiological role of the metallochaperone SlyD is divalent cations binding. Nickel binds only to the FKBP domain but extensively increases the thermodynamic stability of both SlyD domains, verifying the coupled stability of the domains.

Resolving Stability Contributions in the Consensus Tetratricopeptide Repeat

Repeat proteins are constructed from linear arrays of a common structural unit. The physical characteristics that describe the resulting structure depend on the sequence composition of the repeating unit, the number of repeats, and the architectural arrangement of the units with respect to each other1.The tetratricopeptide repeat is 34 amino acids in length, and consists of a pair of anti-parallel “A” and “B” α-helices. Regan and coworkers have designed a consensus TPR (cTPR) sequence and characterized the thermodynamic stability and kinetics of folding of a series of cTPRs (1-10 repeats) with a “solubilizing” C-terminal “S” helix2.3.4. Their stability data were fit using a homopolymeric model in which the A, B, and S helices were treated as energetically equivalent, although there are significant differences in sequence and packing between the A and B helices. Because the A:B helix ratio was the same in all constructs studied, the homopolymeric model was sufficient to model the thermodynamics of unfolding, despite potential intrinsic energy differences between the different helices. Furthermore, the energy associated with each respective interfacial interaction (AiBi+1, BiAi+1,BiSi+1) was not able to be resolved.To determine whether the A and B helices differ in intrinsic stability (ΔGA and ΔGB), and whether interfacial stability (ΔGAB and ΔGBA) values are synonymous, we constructed a series of cTPRs that vary in length, and in the ratio of A to B helices. In addition, we include constructs lacking the C-terminal S-helix. Urea-induced unfolding transitions suggest cooperative folding with a moderate level of nearest-neighbor coupling, as was found by Regan and coworkers. Our results indicate that stability is heterogeneously distributed within cTPR arrays. Although the A and B helices have similar intrinsic stabilities, the energy arising from BiAi+1 interactions contribute more to stability than their AiBi+1 counterparts.

Non-natural amino acid fluorophores for one- and two-step fluorescence resonance energy transfer applications

Fluorescence resonance energy transfer (FRET) provides a powerful means to study protein conformational changes. However, the incorporation of an exogenous FRET pair into a protein could lead to undesirable structural perturbations of the native fold. One of the viable strategies to minimizing such perturbations is to use non-natural amino acid-based FRET pairs. Previously, we showed that p-cyanophenylalanine (Phe CN) and tryptophan (Trp) constitute such a FRET pair, useful for monitoring protein folding–unfolding transitions. Here we further show that 7-azatryptophan (7AW) and 5-hydroxytryptophan (5HW) can also serve as a FRET acceptor to Phe CN, and the resultant FRET pairs offer certain advantages over Phe CN–Trp. For example, the fluorescence spectrum of 7AW is sufficiently separated from that of Phe CN, making it straightforward to decompose the FRET spectrum into donor and acceptor contributions. Moreover, we show that Phe CN, Trp, and 7AW can be used together to form a multi-FRET system, allowing more structural information to be extracted from a single FRET experiment. The applicability of these FRET systems is demonstrated in a series of studies where they are employed to monitor the urea-induced unfolding transitions of the villin headpiece subdomain (HP35), a designed ββα motif (BBA5), and the human Pin1 WW domain.

Using an Amino Acid Fluorescence Resonance Energy Transfer Pair To Probe Protein Unfolding: Application to the Villin Headpiece Subdomain and the LysM Domain

Previously, we have shown that p-cyanophenylalanine (Phe CN) and tryptophan (Trp) constitute an efficient fluorescence resonance energy transfer (FRET) pair that has several advantages over commonly used dye pairs. Here, we aim to examine the general applicability of this FRET pair in protein folding-unfolding studies by applying it to the urea-induced unfolding transitions of two small proteins, the villin headpiece subdomain (HP35) and the lysin motif (LysM) domain. Depending on whether Phe CN is exposed to solvent, we are able to extract either qualitative information about the folding pathway, as demonstrated by HP35, which has been suggested to unfold in a stepwise manner, or quantitative thermodynamic and structural information, as demonstrated by LysM, which has been shown to be an ideal two-state folder. Our results show that the unfolding transition of HP35 reported by FRET occurs at a denaturant concentration lower than that measured by circular dichroism (CD) and that the loop linking helix 2 and helix 3 remains compact in the denatured state, which are consistent with the notion that HP35 unfolds in discrete steps and that its unfolded state contains residual structures. On the other hand, our FRET results on the LysM domain allow us to develop a model for extracting structural and thermodynamic parameters about its unfolding, and we find that our results are in agreement with those obtained by other methods. Given the fact that Phe CN is a non-natural amino acid and, thus, amenable to incorporation into peptides and proteins via existing peptide synthesis and protein expression methods, we believe that the FRET method demonstrated here is widely applicable to protein conformational studies, especially to the study of relatively small proteins.

Folding Mechanism of an Ankyrin Repeat Protein: Scaffold and Active Site Formation of Human CDK Inhibitor p19 INK4d

The p19 INK4d protein consists of five ankyrin repeats (ANK) and controls the human cell cycle by inhibiting the cyclin D-dependent kinases (CDK) 4 and 6. We investigated the folding of p19 INK4d by urea-induced unfolding transitions, kinetic analyses of unfolding and refolding, including double-mixing experiments and a special assay for folding intermediates. Folding is a sequential two-step reaction via a hyperfluorescent on-pathway intermediate. This intermediate is present under all conditions, during unfolding, refolding and at equilibrium. The folding mechanism was confirmed by a quantitative global fit of a consistent set of equilibrium and kinetic data revealing the thermodynamics and intrinsic folding rates of the different states. Surprisingly, the N ↔ I transition is much faster compared to the I ↔ U transition. The urea-dependence of the intrinsic folding rates causes population of the intermediate at equilibrium close to the transition midpoint. NMR detected hydrogen/deuterium exchange and the analysis of truncated variants showed that the C-terminal repeats ANK3-5 are already folded in the on-pathway intermediate, whereas the N-terminal repeats 1 and 2 are not folded. We suggest that during refolding, repeats ANK3–ANK5 first form the scaffold for the subsequent assembly of repeats ANK1 and ANK2. The binding function of p19 INK4d resides in the latter repeats. We propose that the graded stability and the facile unfolding of repeats 1 and 2 is a prerequisite for the down-regulation of the inhibitory activity of p19 INK4d during the cell-cycle.

Multistate Folding of the Villin Headpiece Domain

The villin headpiece (HP67) is a 67 residue, monomeric protein derived from the C-terminal domain of villin. Wild-type HP67 (WT HP67) is the smallest fragment of villin that retains strong in vitro actin-binding activity. WT HP67 is made up of two subdomains, which form a tightly packed interface. The C-terminal subdomain of WT HP67, denoted HP35, is rich in helical structure, folds in isolation, and has been widely used as a model system for folding studies. In contrast, very little is known about the folding of the intact villin headpiece domain. Here, NMR, CD and H/2H amide exchange measurements are used to follow the pH, thermal and urea-induced unfolding of WT HP67 and a mutant (HP67 H41Y) in which a buried conserved histidine in the N-terminal subdomain, His41, has been mutated to Tyr. Although most small proteins display two-state equilibrium unfolding, the results presented here demonstrate that unfolding of the villin headpiece is a multistate process. The presence of a folded N-terminal subdomain is shown to stabilize the C-terminal subdomain, increasing the midpoints of the thermal and urea-induced unfolding transitions and increasing protection factors for H/2H exchange. Histidine 41 has been shown to act as a pH-dependent switch in wild-type HP67: the N-terminal subdomain is unfolded when His41 is protonated, while the C-terminal subdomain remains folded irrespective of the protonation state of His41. Mutation of His41 to Tyr eliminates the segmental pH-dependent unfolding of the headpiece. The mutation stabilizes both domains, but folding is still multistate, indicating that His41 is not solely responsible for the unusual equilibrium unfolding behavior of villin headpiece domain.

A pH‐dependent conformational change in EspA, a component of the Escherichia coli O157:H7 type III secretion system

pH-Dependent structural changes for Escherichia coli O157:H7 EspA were characterized by CD, 8-anilino-2-naphthyl sulfonic acid (ANS) fluorescence, and sedimentation equilibrium ultracentrifugation. Far- and near-UV CD spectra, recorded between pH 2.0 and 7.0, indicate that the protein has significant amounts of secondary and tertiary structures. An increase in ANS fluorescence intensity (in the presence of EspA) was observed at acidic pH; whereas, no increased ANS fluorescence was observed at pH 7.0. These results suggest the presence of a partially unfolded state. Interestingly, urea-induced unfolding transitions, monitored by far-UV CD spectroscopy, showed that the protein is destabilized at pH 2.0 as compared with EspA at neutral pH. Although increased ANS fluorescence was observed at pH 3.0, the urea-induced unfolding curve is similar to that found at pH 7.0. This result suggests the presence, at pH 3.0, of an ordered, but partially unfolded state, which differs from typical molten globule. The results of analytical ultracentrifugation and infrared spectroscopy indicate that EspA molecules associate at pH 7.0, suggesting the formation of short filamentous oligomers containing alpha-helical structures, whereas the protein tend to form nonspecific aggregates containing intermolecular beta-sheets at pH 2.0. Our experiments indicate that EspA has the potential to spontaneously form filamentous oligomers at neutral pH; whereas the protein is partially unfolded, assuming different conformations, at acidic pH.

Nonspecific hydrophobic interactions stabilize an equilibrium intermediate of apomyoglobin at a key position within the AGH region.

Acid-induced unfolding of apomyoglobin (apoMb) proceeds in a multistate process involving at least one equilibrium intermediate (I) at pH 4.2. The structure of the I form has been investigated thoroughly, with significant effort devoted to identifying potentially stabilizing native contacts. Here, we test whether rigid side-chain packing interactions like those in holomyoglobin persist at a buried position, Met-131, within the low-pH apoMb intermediate. We have measured the urea-induced unfolding transitions of overpacking, underpacking, and polar substitutions of Met-131 to determine the effect on the stability of the native and intermediate states of apoMb. Whereas underpacking substitutions should destabilize the I form irrespective of the degree of native side-chain-packing interactions, we anticipate that overpacking replacements might show opposite effects in a tightly packed environment, compared with a region lacking native side-chain packing interactions. We observe that, whereas underpacking and polar substitutions destabilize the I form, overpacking substitutions are stabilizing, implying that I is structurally plastic. We also report a strong correlation between the I state unfolding free energies and side-chain transfer free energies from water to octanol. Our results suggest that, whereas side-chain hydrophobicity is important for the stability of the I form, specific side-chain packing interactions are not.

Contribution to stability and folding of a buried polar residue at the CARM1 methylation site of the KIX domain of CBP.

The transcriptional coactivator and acetyltransferase CREB Binding Protein (CBP) is comprised of several autonomously folded and functionally independent domains. The KIX domain mediates interactions between CBP and numerous transcriptional activators. The folded region of KIX has all the structural features of a globular protein, including three alpha-helices, two short 3(10) helices, and a well-packed hydrophobic core. KIX contains a buried cation-pi interaction between the positively charged guanidinium group of Arg 600 and the aromatic ring of Tyr 640. Arg 600 is a site for regulatory methylation by CARM1/PRMT4, which negates the CREB-binding function of the KIX domain. The role of the Arg 600-Tyr 640 buried polar interaction in specifying and stabilizing the structure of KIX was investigated by comparing the folding of wild-type KIX with the single point mutants Y640F and R600M. The Y640F mutant disrupts a hydrogen bond involving the Tyr 640 OH and the backbone of V595 but still allows for the cation-pi interaction while the R600M mutant disrupts the cation-pi interaction. Both wild type KIX and Y640F exhibit properties expected of native like, globular proteins such as a single oligomerization state (monomer), cooperative thermal and urea-induced unfolding transitions, and a well-packed core. In contrast, the R600M mutant has properties reminiscent of a molten globule state, including a tendency to aggregate, noncooperative thermal unfolding transition, and a loosely packed core. Thus, the buried cation-pi interaction is critical for specifying the unique cooperatively folded structure of KIX.

Complementation of buried lysine and surface polar residues in a designed heterodimeric coiled coil.

The coiled coil is an attractive target for protein design. The helices of coiled coils are characterized by a heptad repeat of residues denoted a to g. Residues at positions a and d form the interhelical interface and are usually hydrophobic. An established strategy to confer structural uniqueness to two-stranded coiled coils is the use of buried polar Asn residues at position a, which imparts dimerization and conformational specificity at the expense of stability. Here we show that polar interactions involving buried position-a Lys residues that can interact favorably only with surface e' or g' Glu residues also impart structural uniqueness to a designed heterodimeric coiled coil with the nativelike properties of sigmoidal thermal and urea-induced unfolding transitions, slow hydrogen exchange and lack of ANS binding. The position-a Lys residues do not, however, confer a single preference for helix orientation, likely reflecting the ability of Lys at position a to from favorable interactions with g' or e' Glu residues in the parallel and antiparallel orientations, respectively. The Lys-Glu polar interaction is less destabilizing than the Asn-Asn a-->a' interaction, presumably reflecting a higher desolvation penalty associated with the completely buried polar position-a groups. Our results extend the range of approaches for two-stranded coiled-coil design and illustrate the role of complementing polar groups associated with buried and surface positions of proteins in protein folding and design.

Protein folding and stability of human CDK inhibitor p19 INK4d

P19 INK4d is a tumor suppressing protein and belongs to a family of cyclin D-dependent kinase inhibitors of CDK4 and CDK6, which play a key role in human cell cycle control. P19 comprises ten α-helices arranged sequentially in five ankyrin repeats forming an elongated structure. This rather simple topology, combined with its physiological function, makes p19 an interesting model protein for folding studies. Urea-induced unfolding transitions monitored by far-UV CD and phenylalanine fluorescence coincide and suggest a two-state mechanism for equilibrium unfolding. Unfolding of p19 followed by 2D 1H- 15N HSQC spectra revealed a third species at moderate urea concentrations with a maximum population of about 30 % near 3.2 M urea. It shows poor chemical shift dispersion, but cross-peaks emerge for some residues that are distinct from the native or unfolded state. This equilibrium intermediate either arises only at high protein concentrations (as in the NMR experiment) or has similar optical properties to the unfolded state. Stopped-flow far-UV CD experiments at various urea concentrations revealed that α-helical structure is formed in three phases, of which only the fastest phase (10 s −1) depends upon the urea concentration. The kinetic of the slowest phase (0.017 s −1) can be resolved by 1D real-time NMR and accelerated by cyclophilin. It is limited in rate by prolyl isomerization, and native-like ordered structure cannot form prior to this isomerization. The two fast phases lead to 83 % native protein within the dead time of the NMR experiment. In contrast to p16 INK4a, which exhibits only a marginal stability and high unfolding rates, p19 shows the expected stability for a protein of this size with a clear kinetic barrier between the unfolded and folded state. Therefore, p19 might complement the function of less stable INK4 inhibitors in cell cycle control under unfavorable conditions.

Modular structure of the trigger factor required for high activity in protein folding

The Escherichia coli trigger factor is a peptidyl-prolyl cis/trans isomerase (PPIase) which catalyzes proline-limited protein folding extremely well. It has been found associated with nascent protein chains as well as with the chaperone GroEL. The trigger factor utilizes protein regions outside the central catalytic domain for catalyzing refolding of unfolded proteins efficiently. Here we produced several fragments which encompass individual domains or combinations of the middle FKBP-like domain (M) with the N-terminal (N) and C-terminal (C) regions, respectively. These fragments appear to be stably folded. They show ordered structure and cooperative urea-induced unfolding transitions, and the far-UV CD spectrum of the intact trigger factor is well represented by the sum of the spectra of the fragments. This suggests that the native trigger factor shows a modular structure, which is composed of three fairly independent folding units. In the intact protein there is a slight mutual stabilization of these units. The high enzymatic activity in protein folding could not be restored by fusing alternatively the N or the C-terminal regions to the catalytic domain (in NM and MC constructs, respectively). Surprisingly, the high folding activity of the intact trigger factor has been regained partially by functional complementation of the overlapping NM and MC constructs.

Urea-Induced Equilibrium Unfolding of Single Tryptophan Mutants of Yeast Phosphoglycerate Kinase: Evidence for a Stable Intermediate

Several single-tryptophan mutants of yeast phosphoglycerate kinase (PGK) have been used in the present study to characterize the urea-induced unfolding of PGK. A possibility that residual structures might be present in the urea-unfolded state was also investigated. The urea-induced unfolding transitions were monitored using circular dichroism (CD) and fluorescence techniques. The presence of stable intermediate(s) during urea-induced unfolding is suggested by biphasic transitions detected for the mutants containing tryptophans in the N-terminal domain and by the noncoincidence of transitions detected by various methods for other mutants. The N-terminal tryptophan probes exhibit hyperfluorescent properties in the intermediate state and a wavelength of maximum emission that lies between that of the native and unfolded state. This unfolding intermediate exhibits a major decrease in the ellipticity at 220 nm, but only a minor decrease at 278 nm, relative to the native state. These results suggest a significant loss of secondary structure content and a relatively small change in the asymmetric environment of tyrosine residues. Increased 1-anilinonaphthalene-8-sulfonic acid binding in the denaturant concentration range corresponding to the N → I transition indicates the presence of a partially folded structure with exposed hydrophobic surfaces. These results demonstrate that the partially folded intermediates detected during urea-induced denaturation are structurally similar to those detected previously during guanidine-induced denaturation. No significant differences were detected between the urea- and guanidine-unfolded proteins on the basis of their fluorescence and CD properties.

Thermodynamic Stability of the Molten Globule States of Apomyoglobin

Whereas horse apomyoglobin is fully unfolded at pH 2 in the absence of salt, addition of a salt such as sodium chloride or sodium trichloroacetate stabilizes the molten globule state. Thermal unfolding of the salt-stabilized molten globule states of horse apomyoglobin at pH 2 measured by far-UV circular dichroism occurs not only on heating (i.e. heat-denaturation) but also on cooling (i.e. cold-denaturation). This demonstrates that a hydrophobic interaction contributes to the stability of the molten globule state and suggests that the unfolding transition can be represented by a cooperative two-state mechanism. To clarify the mechanism of conformational transition, we investigated the thermal unfolding of the chloride-stabilized molten globule state by differential scanning calorimetry. We observed a broad but distinct excess heat capacity peak, which is consistent with the unfolding transition measured by circular dichroism. To further characterize the molten globule states, we examined by far-UV circular dichroism the denaturant-induced unfolding transitions of the molten globule states stabilized by sodium chloride or sodium trichloroacetate. The urea-induced unfolding transitions of the molten globule states were explained by the two-state mechanism. The guanidine-hydrochloride-induced unfolding experiments clarified that the trichloroacetate-stabilized molten globule state is distinct from the chloride-stabilized one and that the former involves additional helical segment(s). These results support a view that the thermal unfolding of the molten globule states at pH 2 can be approximated by a two-state transition. However, several results suggested that a combined mechanism incorporating the two-state transition and a gradual structural change would be more general in describing the conformational transition of the molten globule states. f2 f2 Abbreviations used: H/D, hydrogen-deuterium; NaTCA, sodium trichloroacetate; Gdn-HCl, guanidine hydrochloride; CD, circular dichroism; DSC, differential scanning calorimetry; SAXS, small angle X-ray scattering; R gradius of gyration.