Trapping the on-pathway folding intermediate of Im7 at equilibrium

The four-helical protein Im7 folds via a rapidly formed on-pathway intermediate (k(UI)=3000 s(-1) at pH 7.0, 10 degrees C) that contains three (helices I, II and IV) of the four native alpha-helices. The relatively slow (k(IN)=300 s(-1)) conversion of this intermediate into the native structure is driven by the folding and docking of the six residue helix III onto the developing hydrophobic core. Here, we describe the structural properties of four Im7* variants designed to trap the protein in the intermediate state by disrupting the stabilising interactions formed between helix III and the rest of the protein structure. In two of these variants (I54A and L53AI54A), hydrophobic residues within helix III have been mutated to alanine, whilst in the other two mutants the sequence encompassing the native helix III was replaced by a glycine linker, three (H3G3) or six (H3G6) residues in length. All four variants were shown to be monomeric, as judged by analytical ultracentrifugation, and highly helical as measured by far-UV CD. In addition, all the variants denature co-operatively and have a stability (DeltaG(UF)) and buried hydrophobic surface area (M(UF)) similar to those of the on-pathway kinetic intermediate. Structural characterisation of these variants using 1-anilino-8-napthalene sulphonic acid (ANS) binding, near-UV CD and 1D (1)H NMR demonstrate further that the trapped intermediate ensemble is highly structured with little exposed hydrophobic surface area. Interestingly, however, the structural properties of the variants I54A and L53AI54A differ in detail from those of H3G3 and H3G6. In particular, the single tryptophan residue, located near the end of helix IV, and distant from helix III, is in a distinct environment in the two sets of mutants as judged by fluorescence, near-UV CD and the sensitivity of tryptophan fluorescence to iodide quenching. Overall, the results confirm previous kinetic analysis that demonstrated the hierarchical folding of Im7 via an on-pathway intermediate, and show that this species is a highly helical ensemble with a well-formed hydrophobic core. By contrast with the native state, however, the intermediate ensemble is flexible enough to change in response to mutation, its structural properties being tailored by residues in the sequence encompassing the native helix III.     

Characterization of an associated equilibrium folding intermediate of bovine growth hormone

In the preceding paper [Havel, H. A., Kauffman, E. W., Plaisted, S. M., & Brems, D. N. (1986) Biochemistry (preceding paper in this issue)], an associated intermediate was shown to be highly populated during the equilibrium denaturation of bovine growth hormone. In this paper, we describe its partial characterization and propose a mechanism for association. The associated equilibrium intermediate is populated under conditions that induce partial denaturation and at protein concentrations greater than 0.2 mg/mL. The remaining nativelike helical structure present in the partially denatured species is implicated in the mechanism of association as demonstrated by similar concentration dependencies and thermal stabilities of the helix and the associated equilibrium intermediate. Furthermore, it is suggested that a putative amphiphilic helix from residues 110-127 plays a critical role in the association as demonstrated by a diminution of the associated equilibrium intermediate when mixed with the peptide fragment 96-133. A model is proposed to account for these results in which partial denaturation exposes the segment of the protein corresponding to the hydrophobic face of the putative amphiphilic helix 110-127. This metastable form is the species from which association occurs. Association is stabilized by the hydrophobic interactions resulting from intermolecular packing of the lipophilic faces of the helices. The implications of these results to protein folding studies are described.     

Mechanism of the interaction of human platelet profilin with actin

We have reexamined the interaction of purified platelet profilin with actin and present evidence that simple sequestration of actin monomers in a 1:1 complex with profilin cannot explain many of the effects of profilin on actin assembly. Three different methods to assess binding of profilin to actin show that the complex with platelet actin has a dissociation constant in the range of 1 to 5 microM. The value for muscle actin is similar. When bound to actin, profilin increases the rate constant for dissociation of ATP from actin by 1,000-fold and also increases the rate of dissociation of Ca2+ bound to actin. Kinetic simulation showed that the profilin exchanges between actin monomers on a subsecond time scale that allows it to catalyze nucleotide exchange. On the other hand, polymerization assays give disparate results that are inconsistent with the binding assays and each other: profilin has different effects on elongation at the two ends of actin filaments; profilin inhibits the elongation of platelet actin much more strongly than muscle actin; and simple formation of 1:1 complexes of actin with profilin cannot account for the strong inhibition of spontaneous polymerization. We suggest that the in vitro effects on actin polymerization may be explained by a complex mechanism that includes weak capping of filament ends and catalytic poisoning of nucleation. Although platelets contain only 1 profilin for every 5-10 actin molecules, these complex reactions may allow substoichiometric profilin to have an important influence on actin assembly. We also confirm the observation of I. Lassing and U. Lindberg (1985. Nature [Lond.] 318:472-474) that polyphosphoinositides inhibit the effects of profilin on actin polymerization, so lipid metabolism must also be taken into account when considering the functions of profilin in a cell.     

Reversible folding of rhodanese. Presence of intermediate(s) at equilibrium

For the first time completely reversible unfolding was achieved for guanidinium chloride-denatured rhodanese using a systematically defined protocol. These conditions included beta-mercaptoethanol, lauryl maltoside, and sodium thiosulfate. All components were required to get more than the previous best reactivation with lauryl maltoside of 17% (Tandon, S., and Horowitz, P. (1986) J. Biol. Chem. 261, 15615-15681). Non-coincidental transition curves were obtained by monitoring different parameters including: (i) variation in the activity, (ii) shifts of the fluorescence wavelength maximum, and (iii) variation in ellipticity at 220 nm. The transition followed by the fluorescence wavelength maximum was asymmetric and resolvable into two separate transitions. A thermodynamic analysis was used to define the energetics of the two processes. Studies with the fluorescent "apolar" probe 1,8ANS are consistent with the appearance of organized hydrophobic surfaces following the first transition. Near UV CD measurements indicated that the first transition is associated with a loss of dyssymmetry around at least some of the tryptophans. Thus, the unfolding of rhodanese is complex, and there are detectable intermediate(s) during the process. These results suggest that reversible unfolding occurs in two discrete stages: 1) loss of tertiary interactions and activity, with retention of secondary structure, and 2) loss of secondary structure. The available x-ray structure suggests that the first transition can be associated with changes in the domain interactions, which may modulate the effectiveness of helix dipoles in lowering the pKa of the active site sulfhydryl.     

Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis

It is challenging to experimentally define an energy landscape for protein folding that comprises multiple partially unfolded states. Experimental results are often ambiguous as to whether a non-native state is conformationally homogeneous. Here, we tested an approach combining systematic mutagenesis and a Br?nsted-like analysis to reveal and quantify conformational heterogeneity of folding intermediate states. Using this method, we resolved an otherwise apparently homogeneous equilibrium folding intermediate of Borrelia burgdorferi OspA into two conformationally distinct species and determined their relative populations. Furthermore, we mapped the structural differences between these intermediate species, which are consistent with the non-native species that we previously proposed based on native-state hydrogen exchange studies. When treated as a single state, the intermediate ensemble exhibited fractional Phi-values for mutations and Hammond-type behaviors that are often observed for folding transition states. We found that a change in relative population of the two species within the intermediate ensemble explains these properties well, suggesting that fractional Phi-values and Hammond-type behaviors exhibited by folding intermediates and transition states may arise more often from conformational heterogeneity than from a single partial structure. Our results are consistent with the presence of multiple minima in a rugged energy landscape predicted from theoretical studies. The method described here provides a promising means to probe a complex folding energy landscape.     

Kinetic intermediate in the folding of human prion protein

Transmissible spongiform encephalopathies are associated with the conversion of cellular prion protein, PrP(C), into a misfolded oligomeric form, PrP(Sc). Here we have examined the kinetics of folding and unfolding reactions for the recombinant human prion protein C-terminal fragment 90-231 at pH 4.8 and 7.0. The stopped-flow data provide clear evidence for the population of an intermediate on the refolding pathway of the prion protein as indicated by a pronounced curvature in chevron plots and the presence of significant burst phase amplitude in the refolding kinetics. In addition to its role in the normal prion protein folding, this intermediate likely represents a crucial monomeric precursor of the pathogenic PrP(Sc) isoform.     

Detection of an equilibrium intermediate in the folding of a monomeric insulin analog.

To determine the conformational properties of the C-terminal region of the insulin B-chain relative to the helical core of the molecule, we have investigated the fluorescence properties of an insulin analog in which amino acids B28 and B29 have been substituted with a tryptophan and proline residue respectively, ([WB28,PB29]insulin). The biological properties and far-UV circular dichroism (CD) spectrum of the molecule indicate that the conformation is similar to that of native human insulin. Guanidine hydrochloride (GdnHCl)-induced equilibrium denaturation of the analog as monitored by CD intensity at 224 nm indicates a single cooperative transition with a midpoint of 4.9 M GdnHCl. In contrast, when the equilibrium denaturation is observed by steady-state fluorescence emission intensity at 350 nm, two distinct transitions are observed. The first transition accounts for 60% of the observed signal and has a midpoint of 1.5 M GdnHCl. The second transition roughly parallels that observed by CD measurements with an approximate midpoint of 4.5 M GdnHCl. The near-UV CD spectrum, size-exclusion, and ultracentrifugation properties of [WB28,PB29]insulin indicate that this analog does not self-associate in a concentration-dependent manner as does human insulin. Thus, the observed fluorescence changes must be due to specific conformational transitions which occur upon unfolding of the insulin monomer with the product of the first transition representing a stable folding intermediate of this molecule.     

Evidence for identity between the equilibrium unfolding intermediate and a transient folding intermediate: a comparative study of the folding reactions of alpha-lactalbumin and lysozyme

The refolding kinetics of alpha-lactalbumin at different concentrations of guanidine hydrochloride have been investigated by means of kinetic circular dichroism and stopped-flow absorption measurements. The refolding reaction consists of at least two stages, the instantaneous accumulation of the transient intermediate that has peptide secondary structure and the subsequent slow process associated with formation of tertiary structure. The transient intermediate is compared with the well-characterized equilibrium intermediate observed during the denaturant-induced unfolding. Stabilities of the secondary structures against the denaturant, affinities for Ca2+, and tryptophan absorption properties of the transient and equilibrium intermediates were investigated. In all of these respects, the transient intermediate is identical with the equilibrium one, demonstrating the validity of the use of the equilibrium intermediate as a model of the folding intermediate. Essentially the same transient intermediate was also detected in the folding of lysozyme, the protein known to be homologous to alpha-lactalbumin but whose equilibrium unfolding is represented as a two-state reaction. The stability and cooperativity of the secondary structure of the intermediate of lysozyme are compared with those of alpha-lactalbumin. The results show that the protein folding occurring via the intermediate is not limited to the proteins that show equilibrium intermediates. Although the unfolding equilibria of most proteins are well approximated as a two-state reaction, the two-state hypothesis may not be applicable to the folding reaction under the native condition. Two models of protein folding, intermediate-controlled folding model and multiple-pathway folding model, which are different in view of the role of the intermediate in determining the pathway of folding, are also discussed.     

Structure of stable protein folding intermediates by equilibrium phi-analysis: the apoflavodoxin thermal intermediate

Protein intermediates in equilibrium with native states may play important roles in protein dynamics but, in cases, can initiate harmful aggregation events. Investigating equilibrium protein intermediates is thus important for understanding protein behaviour (useful or pernicious) but it is hampered by difficulties in gathering structural information. We show here that the phi-analysis techniques developed to investigate transition states of protein folding can be extended to determine low-resolution three-dimensional structures of protein equilibrium intermediates. The analysis proposed is based solely on equilibrium data and is illustrated by determination of the structure of the apoflavodoxin thermal unfolding intermediate. In this conformation, a large part of the protein remains close to natively folded, but a 40 residue region is clearly unfolded. This structure is fully consistent with the NMR data gathered on an apoflavodoxin mutant designed specifically to stabilise the intermediate. The structure shows that the folded region of the intermediate is much larger than the proton slow-exchange core at 25 degrees C. It also reveals that the unfolded region is made of elements whose packing surface is more polar than average. In addition, it constitutes a useful guide to rationally stabilise the native state relative to the intermediate state, a far from trivial task.     

Definable equilibrium states in the folding of human prion protein

The role of conformational intermediates in the conversion of prion protein from its normal cellular form (PrP(C)) to the disease-associated scrapie form (PrP(Sc)) remains unknown. To look for such intermediates in equilibrium conditions, we have examined the unfolding transitions of PrP(C), primarily using the chemical denaturant guanidine hydrochloride (GuHCl). When the protein conformation is assessed by NMR, there is a gradual shift of NMR signals in the regions between residues 125-146 and 186-196. The denaturant dependence of these shifts shows that in aqueous solution the native and locally unfolded conformations are both significantly populated. Following this shift, there is the major unfolding transition to generate a substantially unfolded population. However, analysis of NMR chemical shift and intensity changes shows that there is persistent structure in the molecule well beyond this major cooperative unfolding transition. Residual structure within this state is extensive and encompasses the majority of the secondary structure elements found in the native state of the protein.     

Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations

The isothermal equilibrium folding of the unmodified yeast tRNA(Phe) is studied as a function of Na(+), Mg(2+), and urea concentration with hydroxyl radical protection, circular dichroism, and diethyl pyrocarbonate (DEPC) modification. These assays indicate that this tRNA folds in Na(+) alone. Similar to folding in Mg(2+), folding in Na(+) can be described by two transitions, unfolded-to-intermediate-to-native. The I-to-N transition has a Na(+) midpoint of approximately 0.5 M and a Hill constant of approximately 4. Unexpectedly, the urea m-value, the dependence of free energy on urea concentration, for the I-to-N transition is significantly smaller in Na(+) than in Mg(2+), 0.4 versus 1.7 kcal mol(-1) M(-1), indicating that more structure is formed in the Mg(2+)-induced transition. DEPC modification indicates that the I state in Na(+)-induced folding contains all four helices of tRNA and the I-to-N transition primarily corresponds to the formation of the tertiary structure. In contrast, the intermediate in Mg(2+)-induced folding contains only three helices, and the I-to-N transition corresponds to the formation of the acceptor stem plus tertiary structure. The cation dependence of the intermediates arises from the differences in the stability of the acceptor stem and the tertiary structure. The acceptor stem is stable at a lower Na(+) concentration than required for the tertiary structure formation. The relative stability is reversed in Mg(2+) so that the acceptor stem and the tertiary structure form simultaneously in the I-to-N transition. These results demonstrate that formation of the RNA secondary structure can be independent or coupled to the formation of the tertiary structure depending on their relative stability in monovalent and divalent ions.     

An equilibrium folding intermediate detected in the thermal unfolding transition of ribonuclease S by circular dichroism

The thermal-denaturation transition of ribonuclease S (RNAase S) is measured by circular dichroism at 225 nm. Only conformational transitions involving the S-peptide–S-protein complex are detected at this wavelength. Different pathways of thermal unfolding at high and low concentrations are apparent: at low concentrations the temperature of half-completion of denaturation (T_m) varies with concentration. Above a total enzyme concentration of 50 μM, T_m remains constant. The observed data can be explained on the basis of a model where the association–dissociation step occurs between S-peptide and thermally (at least partly) unfolded S-protein. The complex as a whole undergoes a major folding–unfolding transition in the course of which the S-peptide μ-helix appears to be formed. The unfolded complex is well populated in the unfolding transition region for enzyme concentrations of 100 μM or more. The model succeeds in deducing thermodynamic parameters from the thermal denaturation curves in various different ways. The values thus obtained are fully self-consistent and, moreover, consistent with the values for the apparent association constant and apparent association enthalpy as measured in enzyme-dilution experiments and by batch calorimetry.     

Detection and characterization of the intermediate on the folding pathway of human alpha-lactalbumin

To discuss the relation between the folding mechanism and the chemical structure of proteins, the reversible unfolding reactions of human alpha-lactalbumin by acidification and by guanidine hydrochloride at 25 degrees C are studied by means of circular dichroism, difference spectra and pH-jump measurements and are compared with those for bovine alpha-lactalbumin. As shown previously for bovine alpha-lactalbumin, the folding process at neutral pH is not explained by a simple two-state mechanism but involves an intermediate form that has the same amount of helical structures as the native form. The transition between the intermediate and the fully denatured states is too rapid to be measured and corresponds to the helix-coil transition of the backbone. One of the differences of human alpha-lactalbumin from the bovine protein is the remarkable stability of the intermediate at neutral pH, which can be explained by differences in the primary chemical structure. Another difference is the existence at acid pH of an additional helical form, which is more helical than the native form. The transition from this to the intermediate or to the fully denatured one also is shown to resemble the helix-coil transition. The following folding scheme of human alpha-lactalbumin is proposed: formula: (see text). Here N is the native form, and the intermediate is a macroscopic state distributed around the state A3 at neutral pH, while the distribution in the acid and fully denautured states shifts toward Am and A-n, respectively.     

The intermediate compounds between human hemoglobin and carbon monoxide at equilibrium and during approach to equilibrium

The procedure of Perrella et al. (Perrella, M., Benazzi, L., Cremonesi, L., Vesely, S., Viggiano, G., and Rossi-Bernardi, L. (1983) J. Biol. Chem. 258, 4511-4517) for trapping the intermediate compounds between human hemoglobin and carbon monoxide was validated by quantitatively determining during the approach to equilibrium all the species present in a solution containing large amounts of intermediates. An accurate estimate of the intermediate compounds at 50% carbon monoxide saturation in 0.1 M KCl, pH 7, at 22 degrees C, allowed the calculation, according to Adair's scheme, of the four equilibrium constants. At 50% ligand saturation, the pool of intermediate species was about 12% of the total. A slightly greater concentration of tri-liganded than mono-liganded species was found. Carbon monoxide bound to beta chains in slightly greater excess with respect to alpha chains in both the mono- and tri-liganded species. The symmetrical bi-liganded intermediates, alpha 2 beta CO2 and alpha 2CO beta 2, were absent. The nature of the bi-liganded intermediate found to be present in detectable amounts by our technique has yet to be clarified: it could be either the asymmetrical species (alpha beta) (alpha CO beta CO) and (alpha beta CO) (alpha CO beta) or both of them. Such a finding on the functional heterogeneity among the four possible bi-liganded intermediates is consistent with hypotheses of the existence of more than two quaternary structures in the course of ligand binding to hemoglobin.     

The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate

T4 lysozyme has two easily distinguishable but energetically coupled domains: the N and C-terminal domains. In earlier studies, an amide hydrogen/deuterium exchange pulse-labeling experiment detected a stable submillisecond intermediate that accumulates before the rate-limiting transition state. It involves the formation of structures in both the N and C-terminal regions. However, a native-state hydrogen exchange experiment subsequently detected an equilibrium intermediate that only involves the formation of the C-terminal domain. Here, using stopped-flow circular dichroism and fluorescence, amide hydrogen exchange-folding competition, and protein engineering methods, we re-examined the folding pathway of T4-lysozyme. We found no evidence for the existence of a stable folding intermediate before the rate-limiting transition state at neutral pH. In addition, using native-state hydrogen exchange-directed protein engineering, we created a mimic of the equilibrium intermediate. We found that the intermediate mimic folds with the same rate as the wild-type protein, suggesting that the equilibrium intermediate is an on-pathway intermediate that exists after the rate-limiting transition state.     

The equilibrium unfolding intermediate observed at pH 4 and its relationship with the kinetic folding intermediates in green fluorescent protein

Folding mechanisms of a variant of green fluorescent protein (F99S/M153T/V163A) were investigated by a wide variety of spectroscopic techniques. Equilibrium measurements on acid-induced denaturation of the protein monitored by chromophore and tryptophan fluorescence and small-angle X-ray scattering revealed that this protein accumulates at least two equilibrium intermediates, a native-like intermediate and an unfolding intermediate, the latter of which exhibits the characteristics of the molten globule state under moderately denaturing conditions at pH 4. To elucidate the role of the equilibrium unfolding intermediate in folding, a series of kinetic refolding experiments with various combinations of initial and final pH values, including pH 7.5 (the native condition), pH 4.0 (the moderately denaturing condition where the unfolding intermediate is accumulated), and pH 2.0 (the acid-denaturing condition) were carried out by monitoring chromophore and tryptophan fluorescence. Kinetic on-pathway intermediates were accumulated during the folding on the refolding reaction from pH 2.0 to 7.5. However, the signal change corresponding to the conversion from the acid-denatured to the kinetic intermediate states was significantly reduced on the refolding reaction from pH 4.0 to pH 7.5, whereas only the signal change corresponding to the above conversion was observed on the refolding reaction from pH 2.0 to pH 4.0. These results indicate that the equilibrium unfolding intermediate is composed of an ensemble of the folding intermediate species accumulated during the folding reaction, and thus support a hierarchical model of protein folding.     

Molten globule-like folding intermediate of asialofetuin at acidic pH

In our earlier communication on acid-induced unfolding of bovine serum fetuin (BSF), we showed the existence of a molten globule (MG)-like state of BSF at pH 1.8. The MG state was characterized by higher content of secondary structure than native and almost complete loss of tertiary structure and more solvent exposed hydrophobic surface [Biochim. Biophys. Acta 1649 (2003) 164]. In this work we have shown the presence of an MG-like partially folded intermediate of asialofetuin at around pH 1.8, which is much different from the MG state observed in BSF in secondary structure contents. The results show that asialofetuin at pH 1.8 retains approximately 45% secondary structure, as evident from far-UV CD spectra. The near-UV CD spectra showed almost complete loss of tertiary structure. The intrinsic fluorescence and acrylamide quenching of the lone tryptophan residue showed that in acid-induced state, it is buried in the interior in a nonpolar environment. The temperature dependence of far-UV CD signal of asialofetuin at pH 1.8 exhibits a weak cooperative thermal transition. A significant increase in ANS fluorescence showed extensive solvent exposure of nonpolar cluster. Size exclusion chromatography (SEC) indicates a slight increase in the hydrodynamic size of acid-induced protein. These results suggest that asialofetuin at pH 1.8 represents the MG-like folding intermediate. Moreover, our results showed that glycosylation might play a role in stabilization of secondary structure during acid and/or thermal denaturation.     

Cooperative sub-millisecond folding kinetics of apomyoglobin pH 4 intermediate

For small single-domain proteins, formation of the native conformation (N) from a fully unfolded form (U) or from a partially folded intermediate (I) occurs typically in a highly cooperative process that can be described by a two-state model. However, it is not clear whether cooperativity arises early along the folding reaction and whether folding intermediates are also formed in highly cooperative processes. Here, we show that each previously identified step leading apomyoglobin from its unfolded form to its native form, namely, the U <= => Ia, the Ia <= => Ib, and the Ib <= => N reactions, exhibits typical features of a two-state reaction. First, refolding and unfolding kinetics of the earliest U <= => Ia reaction are measurable at pH 4.2 within the urea-induced unfolding transition [Jamin, M., and Baldwin, R. L. (1996) Nat. Struct. Biol. 3, 613-618; Jamin, M., and Baldwin, R. L. (1998) J. Mol. Biol. 276, 491-504], and we report here that sub-millisecond kinetics measured by far-UV circular dichroism (CD), a probe of secondary structure, are similar to those measured by Trp fluorescence, a probe of hydrophobic core formation and chain collapse. These results confirm that folding of the earliest intermediate, Ia, occurs in a highly cooperative process, in which hydrophobic collapse and secondary structure formation occur concomitantly in the A(B)GH core. Second, when the refolding of N is measured at high pH, starting from the acid-unfolded ensemble, the formation of Ia occurs in the mixing time of the sub-millisecond stopped-flow, but the subsequent steps, the Ia <= => Ib and Ib <= => N reactions, exhibit similar kinetics by far-UV CD and Trp fluorescence, indicating that these two late stages of the apoMb folding process also occur in highly cooperative, two-state reactions.     

Substrate-induced activation of a trapped IMC-mediated protein folding intermediate

While several unfolded proteins acquire native structures through distinct folding intermediates, the physiological relevance and importance of such states in the folding kinetics remain controversial. The intramolecular chaperone (IMC) of subtilisin was used to trap a partially folded, stable crosslinked intermediate conformer (CLIC) through a disulfide bond between mutated IMC and subtilisin. The trapped CLIC contains non-native interactions. Here we show that CLIC can be induced into a catalytically active form by incubating it with small peptide substrates. The structure and catalytic properties of the activated crosslinked intermediate conformer (A-CLIC) differ from those of the fully folded enzyme in that A-CLIC lacks any endopeptidase activity toward a large protein substrate. Our results show that a disulfide-linked partially folded protein can be induced to acquire catalytic activity with a substrate specificity that is different from completely folded subtilisin. These results also suggest that protein folding intermediates may also participate in catalytic reactions.