Chemicals

Horse skeletal muscle myoglobin was purchased from Sigma (St. Louis, MO), and a specially prepared reagent grade urea for biochemical use was purchased from Nakalai Tesque Inc. (Kyoto, Japan). All other chemicals were either specially prepared or guaranteed reagent-grade chemicals. An Atago 3T refractometer was used to determine the concentration of urea with a refractive index of 589 nm. H-apoMb was prepared by removing the heme from myoglobin according to the methods of Teale and Uzawa et al. [48,53]. All appropriate solutions were filtered by using a membrane filter (pore size of 0.20 or 0.45 μm) before they were used in the experiments.

Equilibrium fluorescence and circular dichroism measurements and fitting

For fluorescence and circular dichroism (CD) measurements, sample solutions were prepared at pH 6.0, 4.0, and 2.0 as follows. An acid-unfolded protein solution (in HCl at pH 2.0) was passed through a Sephadex G-25 column (PD-10; GE Healthcare) equilibrated with 12 mM sodium citrate at pH 6.0. Sample solutions at pH 6.0 and 4.0 containing various concentrations of urea (0–8.0 M) were prepared by six-fold dilution of the protein stock solution, resulting in a 12 mM sodium citrate buffer containing an appropriate concentration of urea. To prepare the sample solution at pH 2.0, the stock solution (in HCl at pH 2.0) passed through the Sephadex G-25 column was diluted with HCl at pH 2.0. The protein concentration for the fluorescence and CD measurements was 5 μM. Fluorescence emission spectra from 300 nm to 450 nm were recorded on a Jasco FP-777 spectrofluorometer (Tokyo, Japan) using an excitation wavelength of 295 nm at 8°C using circulating water. Equilibrium CD measurements were performed using a Jasco J-600S spectropolarimeter (Tokyo, Japan) with a Peltier device at 0–20°C, and the path length of the sample cuvettes was 1.0 mm. The equilibrium unfolding transition curves were fitted to a three-state model by non-linear least squares fitting [54–56] via a global fitting algorithm in IGOR software (Wavemetrics Inc., Lake Oswego OR). Helix contents were calculated by using the ellipticity values at 222 nm according to Chen et al., Sabelko et al., and Dasmeh and Kepp [51,57,58].

Kinetic measurements and fitting

For CF measurements, the refolding reactions were initiated by two-fold dilution of the acid-unfolded protein solution (in HCl at pH 2.0) with 24 mM sodium citrate containing appropriate concentrations of urea to give a final pH of 6.0 whereas the unfolding reactions were initiated by two-fold dilution of the protein solution (in 12 mM sodium citrate at pH 6.0) with 12 mM sodium citrate (pH 6.0) containing appropriate urea concentrations. The final condition for CF measurements was 20–40 μM h-apoMb/12 mM sodium citrate/0–4.1 M urea at pH 6.0. For SF measurements, the refolding reactions were initiated by six-fold dilution of the protein solution in HCl at pH 2.0 and in 0.8 M urea/12 mM sodium citrate at pH 6.0 with refolding buffer containing 14.4 mM and 12 mM sodium citrate, respectively, and appropriate concentrations of urea. The unfolding reactions were initiated by six-fold dilution of the protein solution in 12 mM sodium citrate at pH 6.0 with unfolding buffer containing 12 mM sodium citrate and appropriate concentrations of urea at pH 6.0. The final condition for SF measurements was 5 μM h-apoMb/12 mM sodium citrate/0–7.6 M urea at pH 6.0. For measurement of refolding and unfolding, time-dependent fluorescence change was monitored using an optical cutoff filter (50% transmittance at 305 nm) with an excitation wavelength at 295 nm. All kinetic experiments were conducted at 8°C. CF measurement was performed as previously described by Shastry et al. [59]. SF measurement were carried out on an Applied Photophysics SX-17 stopped-flow device (Surrey, UK). The dead-times of the CF and SF devices, which were 102–175 μs and 5.3 ms respectively, were calibrated by measuring the bimolecular quenching of N-acetyl-L-tryptophanamide fluorescence with N-bromosuccinimide [60].

The kinetic traces obtained by CF and SF measurements were fitted using non-linear least squares fitting to the following equation: (1) where F_obs (t) and F_eq are the fluorescence intensities at time t of the reaction and at a time after the reaction has reached equilibrium, respectively, and F_i and λ_i are the amplitude and apparent rate constant of the i-th phase (i = 1 and 2 for refolding, and i = 3 and 2 for unfolding). The cumulative amplitudes, which give the fluorescence intensities in the absence of the preceding phases of refolding and unfolding, are defined as F_0R2 = F_eq + F₂ and F_0R1 = F_eq + F₂ + F₁ for the refolding initiated at pH 2.0, and F_0U2 = F_eq + F₂ and F_0U1 = F_eq + F₂ + F₃ for the unfolding (F_eq represents the fluorescence intensity at equilibrium).

Quantitative modeling of kinetics

Standard numeric methods were applied to solve the system of linear differential equations describing a particular kinetic scheme, with IGOR software used to determine the eigenvalues and eigenvectors of the corresponding rate matrix. The kinetic parameters were manually optimized to fit the experimental data. The urea-concentration dependence of the elementary rate constants was assumed to follow Eq 2 [61]: (2) where k⁰_ij is the elementary rate constant in the absence of urea, and m^‡_ij is the corresponding slope. R and T are the gas constant and absolute temperature, respectively. Based on the associated rate matrix, the elementary rate constants and the slopes were explored systematically to model the rate constants and amplitudes obtained from the kinetic measurements and equilibrium unfolding experiments. Free energy diagrams were calculated from the elementary rate parameters obtained. The free energy of the relevant states and the transition states was calculated as a function of the α-value as the reaction coordinate at representative urea concentrations. The α-value was defined by a sum of m^‡_ij from N to a given state normalized by the sum of all m^‡_ij, which is the measure of the change in solvent-accessible surface area relative to N. The activation energy for crossing the barriers between states was calculated as follows: (3) where an arbitrary value of 10⁶ s^-1 was used for the pre-exponential factor, A₀. Details of the quantitative modeling are described in S1 File (Methods in S1 File).

Urea-induced equilibrium unfolding

Fig 2 shows the urea-induced equilibrium unfolding of h-apoMb measured by monitoring the changes in ellipticity at 222 nm (Fig 2A) and the Trp fluorescence emission spectra (300–450 nm) upon excitation at 295 nm (Fig 2B and 2C). The measurements were performed in 12 mM sodium citrate at pH 6.0 and 8°C. These unfolding transition curves were similar to those previously reported for sw-apoMb [30,44]. The transition curves monitored by fluorescence at 310–360 nm exhibited two transitions: one at ~1 M urea with an enhancement and the other at ~2 M urea with a decrease. In contrast, those monitored by fluorescence at >370 nm and ellipticity at 222 nm apparently exhibited a single transition at ~1.5 M and ~1 M urea, respectively. They were fitted by non-linear least squares fitting using a global fitting algorithm [9,55,56] to an equilibrium three-state model consisting of the native (N_eq), equilibrium intermediate (M_eq), and unfolded (U_eq) states as follows: Scheme 1 which yielded a set of global parameters (midpoint urea concentrations of U_eq ↔ M_eq and M_eq ↔ N_eq transitions, C_m1, and C_m2, and the corresponding m-values, m₁ and m₂ for each transition) and local parameters (fluorescence intensities at 300–450 nm and ellipticity at 222 nm for N_eq, M_eq, and U_eq at 0 M urea, and the slope of the baselines). A linear approximation of the urea-dependence of the baseline as well as the thermodynamic stability of each species was based on the work of Pace and that of Santoro and Bolen [55,56]. The thermodynamic parameters are listed in Table 1. The fractions of the three species were also calculated as a function of urea concentration (Fig 2D). At 0 M urea, h-apoMb consisted of a mixture of N_eq (~95%) and M_eq (~5%). The fraction of M_eq increased from ~5% at 0 M urea, at the expense of the fraction of N_eq, until it reached a maximum at 1.3 M urea, which was subsequently followed by a decrease with the increasing fraction of U_eq. We also investigated the stability of h-apoMb vs. temperature to rule out possible cold denaturation [26] at 8°C, the temperature used in this study. Fig A in S1 File shows that ellipticity at 222 nm decreased with temperature down to 4°C, below which cold denaturation occurs. This confirms that h-apoMb maintained its native structure at pH 6.0 and 8°C in the absence of urea.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 2. Urea-induced equilibrium unfolding of h-apoMb in 12 mM sodium citrate at pH 6.0 and 8°C.

Unfolding transition curves monitored by (A) ellipticity at 222 nm and (B) the tryptophan fluorescence spectrum (310–440 nm). The solid lines are unfolding transition curves predicted by the global fitting of a three-state model (Scheme 1) along with the residuals (upper panel). (A) Broken lines are baselines of N_eq (blue), M_eq (green), and U_eq (red) predicted by the global fitting. (B) Unfolding curves are coded with different colors. (C) A collection of fluorescence spectra of h-apoMb as a function of urea concentration measured at pH 6.0 and 8°C. Black circles represent an unfolding transition curve monitored by the fluorescence emission at 360 nm. The transition curves in (B) were obtained by transposing data in (C). (D) The fractions of each species as a function of the urea concentration obtained by the equilibrium unfolding experiments. The fractional N_eq, M_eq, and U_eq are shown in blue, green, and red, respectively.

https://doi.org/10.1371/journal.pone.0134238.g002

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Table 1. Thermodynamic parameters for urea-induced equilibrium unfolding of hapoMb at pH 6.0 and 8°C.

https://doi.org/10.1371/journal.pone.0134238.t001

The tryptophan fluorescence spectra and ellipticity at 222 nm of N_eq, M_eq, and U_eq linearly extrapolated to 0 M urea were obtained as local parameters of the global fitting (Fig B in S1 File). At 0 M urea, the fluorescence spectrum and the ellipticity at 222 nm resembled those of N_eq derived from the global fitting, which confirms that N_eq is the dominant species at 0 M urea, pH 6.0, and 8°C. The ellipticity value at 222 nm estimated for N_eq would be slightly less than that at neutral pH because of the local destabilization of the helices [25,62]. The fluorescence spectrum and ellipticity at 222 nm of M_eq derived from the global fitting were similar to those of the predominant equilibrium intermediate at pH 4 (i.e., the pH 4 intermediate). Indeed, the helix contents of M_eq, calculated using the ellipticity at 222 nm, were only ~5% lower than those of the pH 4 intermediate (Table A in S1 File). The slight reduction may have arisen due to the local destabilization of the helices or from the ambiguity in the slope of the baseline of M_eq, which was not well defined because of the apparent single-step transition curve monitored by ellipticity. In addition, the overall structure of these h-apoMb intermediates was indicated to be similar to that of the pH 4 intermediate of sw-apoMb because 1) helix contents were similar (~0.4 for sw-apoMb [33]) and 2) amino acid sequences between h- and sw-apoMbs were highly homologous, albeit with slightly less helix propensity for h-apoMb (Table B in S1 File). This finding is supported by a previous molecular dynamics simulation study of the unfolding of sperm whale and horse myoglobin [51], which indicated an overall structural similarity of the intermediates transiently accumulated in thermal unfolding (although some difference from the apo-proteins was observed in the unfolding of the D/E-helix regions due to the presence of heme). The fluorescence spectrum and ellipticity of U_eq were more similar to those at pH 2.0 than to those at ~8 M urea and pH 6.0. Indeed, the helix contents estimated by the ellipticity values of U_eq were almost identical to those at pH 2.0 at 222 nm, with only 1% difference observed (Table A in S1 File). They were also consistent with those of the acid unfolded state of sw-apoMb at pH 2.3 (~0.1 for sw-apoMb [33]). These results provide further indication that the overall residual structure of U_eq is similar to that of the acid unfolded state of sw-apoMb. In contrast, almost no residual secondary structure was expected for the unfolded state at ~8 M urea. It should be noted that the differences in fluorescence intensity and CD properties between U_eq and ~8 M urea were expected from the slope of the baselines in the unfolding region.

Urea-concentration dependence of the refolding and unfolding kinetics

The refolding and unfolding kinetics of h-apoMb was measured by monitoring fluorescence at various urea concentrations, pH 6.0, and 8°C. The refolding reaction at pH 6.0 was initiated by mixing acid-unfolded protein (pH 2.0) with buffer containing appropriate concentrations of urea, whereas the unfolding reaction at pH 6.0 was initiated by mixing native protein (pH 6.0) with buffer containing appropriate concentrations of urea. CF and SF experiments were combined to cover the time course of folding and unfolding over the time range from ~100 μs to minutes. The dead-times of the CF and SF measurements were 102–175μs (depending on the in-house constructed mixers used in the CF experiments) and 5.3 ms, respectively. Representative kinetic traces of the refolding and unfolding reactions are shown in Fig 3. For the refolding reaction, the kinetic traces measured at urea concentrations (≤1.6 M) were fitted to a double-exponential function consisting of a faster rising phase and a slower decreasing phase whereas those at higher urea concentrations were fitted to a rising single-exponential function. The transient increase and subsequent decrease in fluorescence observed in refolding experiments at low urea concentrations reflects the rapid accumulation of a kinetic intermediate (M; see below) followed by conversion into the native state (0.1–1 s). In contrast, the increase in fluorescence without the slower decreasing phase observed at higher urea concentrations indicates that the kinetic intermediate remained populated as an equilibrium intermediate, M_eq. The observation indicates that the kinetic intermediate was continuously converted into M_eq as the final urea concentration increased, and that both M and M_eq were formed by the same kinetic mechanism from the preceding state even under considerably different conditions (i.e., M transiently accumulated even in the absence of urea, whereas M_eq was stably populated even at urea concentrations higher than 2 M; see below). In addition to the kinetic phase(s) resolved by the fitting, an unresolved change in fluorescence (burst phase) was observed in the CF measurements from 0 M to 3.0 M urea, indicating accumulation of an additional intermediate, I, within the 100-μs range (see below). We also measured the refolding kinetics initiated at pH 6.0 and 0.8 M urea, where M_eq is a major non-native species (Fig 2D), by mixing the protein solution with buffer containing appropriate concentrations of urea in the SF device. In this case, the kinetic trace was fitted to a single-exponential function (0.13–0.53 M urea). This refolding reaction was dominated by the conversion of M_eq to N_eq. The kinetic traces of the unfolding reaction were fitted to a double-exponential function at intermediate urea concentrations (3.0–4.0 M urea) and a single-exponential function at lower and higher concentrations. The transient enhancement of the fluorescence observed at 3–4 M urea (within 1 ms of unfolding) corresponds to the accumulation of a kinetic unfolding intermediate (N'; see below), which is subsequently converted into the unfolded state (0.01–0.1 s). The faster phase was not observed at low urea concentrations because of its small amplitude. It should be noted that urea was limited to ~4 M in the final conditions for CF unfolding measurement because of the solubility of urea and the 1:1 mixing ratio of the CF device.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 3. The kinetic traces of refolding and unfolding reactions of h-apoMb.

The kinetic traces of (A) refolding and (B) unfolding reactions were measured by CF and SF fluorescence methods at various urea concentrations, pH 6.0, and 8°C. The fluorescence intensity is scaled relative to the fluorescence at pH 2.0. Black and colored lines show the kinetic traces obtained by non-linear least squares fitting and by the kinetic modeling, respectively. Kinetic parameters used to reconstruct kinetic traces are shown in Table C in S1 File (elementary rate constants and kinetic m-values) and Table 2 (intrinsic fluorescence intensity of each structural species).

https://doi.org/10.1371/journal.pone.0134238.g003

Fig 4A shows the urea-dependence of the rate constants for folding and unfolding (chevron plot). For refolding initiated at pH 2.0, the slower decreasing phase (phase 2; λ₂ ≈ 2–5 s^-1) corresponds to the rate-limiting step of the overall folding reaction [48,63]. This is consistent with the finding that the rate constant of the slower unfolding phase coincides with λ₂ at matching urea concentrations. The only phase observed in refolding initiated at 0.8 M urea and pH 6.0 (phase 2'; λ_2' ≈ 2–5 s^-1) also overlaps with λ₂ under matching conditions (Fig 4A), indicating that M_eq and the kinetic intermediate overcome a common rate-limiting step in the urea-induced folding process. On the other hand, the faster increasing phase in refolding initiated at pH 2.0 (phase 1; λ₁ ≈ (0.4–1.2) × 10⁴ s^-1) corresponds to the formation of a kinetic intermediate (M). The refolding limb exhibits a slight curvature (rollover) at low urea concentrations (~0.8 M urea), suggesting accumulation of an additional intermediate (I) within the dead-time of the CF measurements. The faster of the two unfolding phases observed at 3–4 M urea (phase 3; λ₃ ≈ 4 × 10³ s^-1) is distinct from λ₁, indicating the formation of a kinetic unfolding intermediate (N'). The accumulation of N' also accounts for the rollover of the unfolding limb of λ₂ at ~3.5 M urea. Transient accumulation of a kinetic unfolding intermediate has previously been reported during the pH-induced unfolding of sw-apoMb [52,64]. Native-like unfolding intermediates are assumed to account for the rollover of the unfolding limb for some proteins [65–67]. However, in contrast to N' (and the reported unfolding intermediate of sw-apoMb), these unfolding intermediates have negligible population during refolding and unfolding because they are always less stable than others under these conditions. The structural and kinetic properties of N' remain to be elucidated.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 4. Urea-dependence of the rate constants and the cumulative amplitudes of refolding and unfolding of h-apoMb and the results obtained by the quantitative modeling.

(A) Urea-dependence of the rate constants of refolding/unfolding reactions obtained in CF and SF experiments (circles): λ₁ (green), λ₂ (blue for refolding and red for unfolding), λ_2' (cyan), and λ₃ (orange). Black and colored solid lines show the rate constants (λ₁, λ₂, and λ₃) and elementary rate constants, respectively, predicted by the quantitative modeling (color codes for the elementary rate constants are shown). (B) The cumulative amplitudes obtained in the CF and SF experiments (circles). Open circles: F_0R1 (green) and F_0R2 (blue) for refolding, and F_0U1 (orange) and F_0U2 (red) for unfolding. Filled circles: F_eq obtained by refolding (blue) and unfolding (red). The solid lines represent F_eq (black), F_0R1 (green), F_0R2 (blue), F_0U1 (orange), and F_0U2 (red) reproduced by quantitative modeling. Here, the cumulative amplitudes are defined as F_0R2 = F_eq + F₂ and F_0R1 = F_eq + F₂ + F₁ for the refolding reaction initiated at pH 2.0, and F_0U2 = F_eq + F₂ and F_0U1 = F_eq + F₂ + F₃ for the unfolding reaction, where F_i is the amplitude of the i-th phase of Eq 1 and F_eq represents the fluorescence intensity at equilibrium. Dashed lines represent the fluorescence intensities of U (red), I (orange), M (green), N' (cyan), and N (blue) predicted by the quantitative modeling. (C) The fractions of each state reproduced by the quantitative modeling. The solid lines represent the reproduced fractions of U (red), I (orange), M (green), N' (cyan) and N (blue), while the dotted lines in pale colors represent the fractional U_eq (red), M_eq (green), and N_eq (blue) obtained by the equilibrium unfolding experiments.

https://doi.org/10.1371/journal.pone.0134238.g004

The observed urea-dependent amplitudes of folding and unfolding reactions provide complementary information on refolding/unfolding kinetics (Fig 4B). We considered cumulative amplitudes (F_0R1, F_0R2 F_0U1, and F_0U2) instead of individual amplitudes (F_i for the i-th phase) for the analysis of fluorescence intensity [11]. The urea-dependence of the equilibrium values, F_eq, is consistent with the equilibrium unfolding transition curves already described (Fig 2). The transition curves obtained for the refolding and unfolding kinetics coincide with each other, which confirms the reversibility of the folding reactions. Because phase 2 is approximately four orders of magnitude slower than phase 1, the urea-dependence of F_0R2 approximates the pre-equilibrium unfolding of M. The urea-dependence of F_0R2 and F_eq shares the transition region at ~1.6 M urea, indicating that the stability of M and M_eq is similar. The F_0R1 values are the fluorescence intensity extrapolated to t = 0 for CF measurements. The discrepancy between F_0R1 and the fluorescence intensity expected for the unfolded state (U) is consistent with the accumulation of I as the burst phase over a urea concentration range from 0 M to ~3 M. Thus, the urea-dependence of F_0R1 approximates the pre-equilibrium unfolding of I. F_0U2 apparently exhibits two small but distinct transitions at ~1.6 M and ~4 M urea. The first transition arises from the unfolding of M_eq populated at 0 M urea (Fig 2D), whereas the second transition arises from the pre-equilibrium between the native state (N) and N'.

Quantitative modeling of the refolding/unfolding kinetics

We quantitatively modeled the folding scheme to reproduce the observable rate constants (λ₁, λ₂, and λ₃) and kinetic amplitudes (F_0R1, F_0R2, F_0U1, and F_0U2). As previously reported, the kinetic behavior of the folding and unfolding reactions of apoMb was consistent with a sequential mechanism rather than a parallel-pathway mechanism [5,45,47,63]. For example, a folding scheme with phases 1 and 2 located on the respective parallel pathways would not account for the enhancement of fluorescence during refolding under strongly native conditions [46]. In support of the sequential pathway mechanism, previous pulsed H/D exchange and double-jump mixing experiments using sw-apoMb revealed that the native state had not populated within a few milliseconds of the pH-induced folding reaction (see Discussion). Based on the current results for h-apoMb, at least five states were associated with its folding/unfolding. In addition to N and U, at least one intermediate (I) is responsible for the observed burst phase in the CF refolding measurements and the rollover of λ₁ at ~0.8 M urea, a second intermediate (M) is responsible for phase 1, and a third intermediate (N') for phase 3 and the curvature of λ₂ at ~3.5 M urea (Fig 4). Thus we assumed a sequential five-state (Scheme 2) in the quantitative modeling described below.

Scheme 2

The elementary rate constants, k_ij, are defined by Eq 2 [61]. The elementary rate constants in the absence of urea, k⁰_ij, and urea-dependence, m^‡_ij, were manually varied to reproduce the chevron plot obtained using the rate-matrix approach. The predicted kinetic parameters are plotted in Fig 4A and listed in Table C in S1 File. As described above, phase 1 was associated with the interconversion between U, I, and M. The unfolding limb of λ₁ was well approximated by k_MI, whereas k_UI, k_IU, and k_IM were constrained by the approximate relationship λ₁ ≈ k_UI/(k_UI + k_IU) × k_IM for the curved refolding limb. Only the ratio for k_UI and k_IU was uniquely determined because the interconversion between U and I occurred within the dead-time of the CF measurements and thus, was not directly observed. On the other hand, phases 2 and 3 were associated with the interconversion between M, N', and N. The urea-dependence of λ₂ was well approximated by k_MN' and k_N'M under native conditions (the refolding limb) and strongly denaturing conditions (the unfolding limb at high urea concentrations), respectively. The elementary rate constants, k_NN' and k_N'N were determined to reproduce the unfolding limb of λ₂ by the approximate relationship λ₂ ≈ k_NN'/(k_NN' + k_N'N) × k_N'M. The urea-dependence of λ₃ at 3–4 M urea gave further constraint to k_NN'. In addition, the fluorescence intensity of each species was optimized to reproduce the amplitudes. The fluorescence intensities of U and N were determined according to the corresponding baselines obtained experimentally. F_0R1 was the fluorescence intensity of the burst phase and F_0R2 approximated the fluorescence intensity transiently saturated after phase 1, in which M was most populated during refolding. Thus, under stabilizing conditions, F_0R1 and F_0R2 were used to determine the fluorescence intensity of I and M, respectively. F_0U2 was reproduced by adjusting the fluorescence intensity of N'. The fluorescence intensity of each species is plotted in Fig 4B and listed in Table 2.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Table 2. Fluorescence intensity of each species (relative to that at pH 2.0) at pH 6.0 and 8°C.

https://doi.org/10.1371/journal.pone.0134238.t002

To test the validity of the model, the obtained kinetic parameters and fluorescence intensities were used to reproduce the kinetic traces of folding and unfolding reactions at representative urea concentrations (Fig 3). The kinetic traces were in good agreement with those obtained experimentally. With 1.5 M and 2.0 M urea, small deviations were observed in the submillisecond range for the kinetic traces of refolding, which could be attributed to the fluctuation in F_0R1 values (Fig 4B). Rapid decreases in fluorescence occurring within ~10 μs of refolding and ~50 μs of unfolding arose from the formation of I and the unfolding of M_eq populated at 0 M urea, respectively. Additionally, thermodynamic parameters calculated using kinetic parameters were in good agreement with those obtained by the fitting of equilibrium unfolding data (Table 2 and Fig 4C). Based on the fluorescence properties of each species, and because some of the species in Scheme 2 were not resolved in the equilibrium unfolding, we assigned the sum of U and I to U_eq, the sum of N' and N to N_eq, and M to M_eq. Taken together, the results of the quantitative modeling accounted for the refolding/unfolding kinetics and equilibrium unfolding data obtained experimentally. Although the five-state model (Scheme 2) was consistent with the data obtained by the kinetic and equilibrium experiments, we further tested whether simpler models could account for the data. For this purpose, we explored the kinetic parameters and fluorescence intensities of each species to reproduce the folding and unfolding kinetics and unfolding equilibrium obtained by the experiments; this was achieved by assuming four-state kinetic schemes lacking one of the intermediates (I, M or N'). The urea-dependence of the rate constants, cumulative amplitudes and population of each species at equilibrium obtained via the quantitative modeling assuming the four-state models are shown in Fig D in S1 File. The discrepancy between the results obtained in the experiments and in the quantitative modeling (assuming a four-state model) lends support to the validity of the five-state kinetic scheme (Scheme 2).

Relationship between the kinetic intermediate M and the equilibrium intermediate M_eq

The relationship between kinetic and equilibrium intermediates has been investigated for several proteins by comparing the structural and thermodynamic properties of the two types of states [3–11]. Such comparative studies have been extensively conducted, in most cases to assess the intermediates of apoMb for pH-induced folding and unfolding. H/D exchange NMR studies on sw-apoMb showed that the equilibrium state(s) populated at pH 4 and a transient kinetic intermediate formed in ~10 ms of refolding at pH 6 exhibited similar patterns of protection, i.e., both intermediates contained native-like secondary structures in the A-, G- H-, and part of the B-, helices [5–7,29,34]. For h-apoMb, time-resolved CD and small angle X-ray scattering (SAXS) experiments revealed that the helix content (~40% compared with the native state) and overall molecular size (~30% larger radius of gyration, R_g, than the native state) were also similar for a kinetic intermediate (I₂) and a trichloroacetate stabilized equilibrium intermediate [48]. Additionally, a slow folding phase with similar rate and amplitude was observed in folding experiments on sw-apoMb starting from either fully unfolded state or the partially folded state at pH 4, indicating that these intermediates were converted into the native state via a common kinetic mechanism [46]. For urea-induced folding of apoMb, Samatova et al. measured urea-dependence of the folding/unfolding of sw-apoMb and the variants using stopped-flow fluorescence under conditions similar to those used in the present study (pH 6.2 and 11°C) [44]. They measured the apparent rate constants of the rate-limiting step of refolding over a wide range of urea concentrations, which was most likely to correspond to λ₂ in the present study (Fig 4A), and the burst phase of refolding (the fluorescence change that occurred within the dead time of the stopped-flow apparatus (<< 20 ms)). The burst phase in their study was likely to correspond to F_0R2 (Fig 4B) in our study. However, the formation of kinetic intermediates and non-native equilibrium states has not been directly compared under a wide range of conditions from strongly native to denaturing, in part due to the limited time resolution of conventional stopped-flow methods.

In this study, we showed that the same set of kinetic barriers were encountered in the formation of the kinetic intermediate (M) and the corresponding equilibrium state (M_eq) for urea-induced folding and unfolding. In particular, we showed, using CF and SF methods (Fig 4), that M shifts from a transient intermediate to a well populated equilibrium state as the urea concentration is increased. In the refolding reaction, M transiently accumulated during refolding at pH 6.0 and 0 M urea, and formation of M was continuously observed in the refolding up to 2.2 M urea as long as the fast phase λ₁ had measurable amplitude. In contrast, the formation of N was observed only at <~1.6 M urea due to the low stability of N (the free energy difference between N and M is ~1.0 kcal/mol at pH 6.0 and 0 M urea; see Table 1). It follows that M predominantly accumulates as an equilibrium intermediate between 0.7 and 2.0 M urea, a urea concentration range in which N is no longer populated predominantly at equilibrium. More intuitively, at low urea concentrations, M was preferentially formed over I because k_IM >> k_MI, and N', which is readily converted into N, was preferentially formed over M because k_MN' is larger than the apparent unfolding rate constant (λ₂ ≈ k_NN'/(k_NN' + k_N'N) × k_N'M); this leads to the conversion of U to N with transient accumulation of M as a kinetic intermediate. In contrast, at 0.7–2 M urea, M was preferentially formed not only over N' because λ₂ was larger than k_MN' but also over I because k_IM >> k_MI; thus, M is stably populated as an equilibrium state, which is equivalent to M_eq. Therefore, M and M_eq are formed by overcoming the same set of kinetic barriers, consistent with a single molecular species. Furthermore, the stability of N relative to M determines whether M transiently accumulates during refolding under strongly native conditions (~0 M urea) or is populated at equilibrium under moderately denaturing conditions (0.7–2.0 M urea). Moreover, the matching urea dependence of λ₂ and λ₂' indicates that M and M_eq is converted into N via the same kinetics process, as previously reported for the pH-induced folding of sw-apoMb [46]. Quantitative modeling also revealed that M and M_eq had similar thermodynamic stabilities and fluorescence intensities (Fig 3A, Tables 1 and 2). This is supported by the shared transition region of F_0R2 and F_eq at ~1.6 M urea because the urea dependence of F_0R2 represented the pre-equilibrium unfolding of M. The energetics of the (un)folding reaction are schematically illustrated by a free energy diagram as a function of α-value, a measure of the change in solvent-accessible surface area occurring during folding. Fig 5 shows that M is one of the most stable species at 1–2 M urea, which leads to the accumulation of M as an equilibrium intermediate. This implies that regions that are more robust to perturbation by urea form at an earlier stage of folding, which further supports the validity of the use of equilibrium intermediates as counterparts for kinetic intermediates. It should be noted that formation of the overall native-like structure (i.e., folding of the C-, D-, E- and part of the B-helix regions that are less stable than the A-, G-, and H-helix regions) would occur during the M → N conversion (phase 2) considering the similarity in the rate-limiting step of folding between h-apoMb and sw-apoMb.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 5. A free energy diagram of h-apoMb at pH 6.0 and 8°C as a function of α-value (i.e., the change in the solvent accessible surface area relative to N).

https://doi.org/10.1371/journal.pone.0134238.g005

Burst phase intermediate, I

A kinetic intermediate, I, accumulates during folding within the dead-time of CF measurements, as indicated by the rollover in λ₁ and the missing amplitude in refolding experiments at low urea concentrations. Quantitative modeling showed that the I state has lower fluorescence than U (0.80 vs. 1.25) and an α-value closer to that of M than U (Fig 5). These results suggest the overall structure of I is already rather compact, consistent with the observation that a considerable decrease in R_g (~6 Å) occurs within ~300 μs of refolding [48].

Our results are also supported by a recent study on the folding of the apo-form of the heme-binding domain of flavohemoglobin (apoHmpH) from Escherichia coli, a protein with a globin fold structurally analogous to h-apoMb [68]. ApoHmpH, which has a single-Trp at position 120 in the H-helix, forms a kinetic intermediate during folding on the 10-μs time scale. Because the fluorescence spectrum of the intermediate is blue-shifted compared to that of the unfolded state, the observed fluorescence quenching is attributed to the establishment of specific short-range intramolecular interactions with quenching residues located in the core region around the Trp residue. This quenched and blue-shifted fluorescence of apoHmpH I-state is consistent with the reduced fluorescence intensity of I observed in our study. Although they are located in different helices, the Trp residues of both proteins are involved in the core region consisting of A-, G-, and H-helices. Thus, the change in Trp fluorescence that occurs during early folding is likely to represent similar structural events for both proteins. In addition, infrared (IR) spectroscopy and UV resonance Raman (UVRR) scattering studies on h-apoMb indicate that both solvated and buried helices are present, but the side-chains of Trp residues are partially solvent-shielded over a time scale of 100 μs [63,69]. Thus, both of these globins rapidly form an intermediate with a quenched and blue-shifted fluorescence spectrum consistent with a collapsed state with a partially formed A-, (B-), G-, and H-helix core.

Folding mechanism of h-apoMb

We showed that a sequential five-state mechanism (Scheme 2) quantitatively accounts for the three observable kinetic phases along with the burst phase in refolding (Figs 3 and 4). Multiphasic folding/unfolding kinetics is, however, also observed for a parallel-pathway folding mechanism, as mentioned above. Here, we discuss the folding mechanism that appropriately represents the folding of h-apoMb. Previous pulsed H/D experiments combined with mass spectrometry on sw-apoMb folding [45, 70] showed that the pH-induced kinetic folding intermediate had already accumulated within 6 ms of initiating folding without detectable amounts of the native state, whereas the native state appeared only after 100 ms of folding at the expense of the intermediate state. This indicates that the folding of sw-apoMb is consistent with a sequential rather than a parallel-pathway mechanism. The sequential mechanism is also supported as a folding mechanism for h-apoMb as indicated by the results of previous continuous-flow CD and SAXS experiments [48]. In these studies, two kinetic phases with time constants of 5 and 49 ms were detected along with a burst phase (dead-time of 280 μs) during pH-induced refolding from pH 2.2 to pH 6.0. The observation that R_g remained constant (23.7 Å) from 300 μs to ~10 ms suggested that h-apoMb folds to the native state via a sequential mechanism with accumulation of two folding intermediates; in contrast, a parallel-pathway mechanism would predict a considerable reduction of R_g over this time range, since both pathways lead to the compact native state. The observed stepwise increase in α-helical content and reduction in R_g in each kinetic phase further support sequential accumulation of two folding intermediates. In addition, a previous ultra-fast H/D exchange experiment on sw-apoMb [5] revealed that the amide protons in the A-, G-, and H-helix regions of the native structure were already protected within 400 μs of pH-induced folding followed by protection of amide protons in the B-, C-, and E-helix around 6 ms. Taken together, the folding of h-apoMb is most likely represented by a sequential rather than a parallel-pathway mechanism, assuming that the folding mechanisms are conserved between sw-apoMb and h-apoMb.

A stepwise change in structure was also observed in previous molecular dynamics simulations [49–51]. Unfolding simulations induced by protonation of ionizable groups, which corresponds to acid unfolding, indicated that sw-apoMb unfolds via partially unfolded structures similar to the pH 4 intermediate, i.e., before it reaches a fully unfolded state, A-, G-, H- and part of B-helices form a compact core with helix contents consistent with those obtained in an experimental study [33]. Thermal unfolding simulations of myoglobins, including sperm whale and horse myoglobins, also demonstrated transient formation of partially unfolded structures with a few helix regions partially formed during thermal unfolding at 500 K (although helix regions relevant to heme binding unfolded more slowly than the apo-proteins due to the presence of heme). In these simulation studies, partially unfolded structures were observed, which suggests that this protein folds via a sequential mechanism.

In Scheme 2, the three intermediates were assumed as on-pathway states, i.e., they were productive intermediates. Here, we also consider the possibility that an intermediate is a dead-end product under the assumption of a five-state sequential scheme. In this case, the intermediate is not productive and should be at least partially unfolded to reach the native state. We therefore ask whether I or M could be an off-pathway intermediate as follows: Scheme 3

The kinetic behavior predicted by Scheme 3 is essentially indistinguishable from that of Scheme 2. This is because pre-equilibrium among U, I, and M is established very rapidly (within ~ms), whereas the conversion to N' becomes significant where the time scale is 100-ms to seconds. The difference between these schemes could be kinetically distinguished if the U ↔ I interconversion was not only experimentally observed but also strongly coupled with the I ↔ M interconversion, as previously reported for the folding of immunity protein 7 [71]. However, the α-values of I and M are expected to be ~50% according to the above schemes, which indicates that I/M should be globally unfolded before the conversion into N within the submillisecond range. This is unlikely when considering that the native-like substructure is already formed on the 400-μs time scale of refolding of the homologous sw-apoMb [5]. Thus, we propose that Scheme 2 represents the folding of h-apoMb but acknowledge that further improvements in time resolution will likely provide additional insight into the folding of this protein.

We observed the formation of a single folding intermediate (M) in the submillisecond-to-millisecond range during refolding. In contrast, some previous kinetic studies of both h-apoMb and sw-apoMb reported two folding intermediates that resulted in sequential four-state kinetic schemes [46,48]. According to previous CD, SAXS, and IR absorption-detected CF experiments on h-apoMb [48,63], the two intermediates exhibited similar secondary structure and overall size. Additionally, the intermediates of sw-apoMb (Ia/Ib) also had similar fluorescence intensities, although UVRR-detected CF measurements of h-apoMb suggested differences in the local environment of the two Trp side-chains [69]. Thus, even if the kinetic intermediate ensemble (M) observed for h-apoMb in this study consisted of multiple forms (such as Ia and Ib), their fluorescence intensities might be similar in the case of h-apoMb, which would make it difficult to resolve them via the Trp fluorescence measurements employed here. Another possibility is that I and M corresponded to Ia and Ib, respectively. As already discussed, it is likely that M involves Ib because the folding from these intermediates is the rate-limiting step and the rate constants (λ₂ ≈ 2 s^-1 at 0 M urea, pH 6.0, and 8°C) are comparable to those obtained in previous studies (~5 s^-1 for sw-apoMb at pH 6.0 and 5°C; ~20 s^-1 for h-apoMb at pH 6.0 and 26°C) given the differences in sequence and temperature. However, the rate constant of the conversion from I to M (λ₁ ≈ 10⁴ s^-1 at 0 M urea, pH 6.0, and 8°C) was two-to-three orders of magnitude larger than the rate constants of the conversion between Ia and Ib (~ 50 s^-1 for sw-apoMb at pH 6.0 and 5°C; ~200 s^-1 for h-apoMb at pH 6.0 and 26°C). This difference is too large to confidently assign phase 1 to the conversion from Ia to Ib. The I ↔ M interconversion is more likely to correspond to conversion of the burst phase intermediate to a folding intermediate observed in previous studies of pH-induced folding of h-apoMb using IR absorption- and UVRR-detected CF [63, 69]. In fact, the burst phase intermediates and I were formed within a similar time range (<100–200 μs), and the folding intermediate formed was indicated to correspond to Ia when observed by IR. However, their rate constants were 2.5−3×10³ s^-1 at 20–25°C, which are much slower than those obtained in this study considering the temperature used here (8°C). Nevertheless, the I ↔ M interconversion is more likely to correspond to the kinetics detected in the submillisecond time range by the IR and UVRR measurements than the Ia ↔ Ib interconversion, although detailed investigation is needed to understand the early folding events of apoMb.

This study is complementary to a recent study on the folding/unfolding kinetics of the intermediates of sw-apoMb at pH 4, since the pH 4 intermediate is analogous to M_eq, based on its spectroscopic properties (Tables A and B, and Fig B in S1 File) [52]. Two intermediates were observed in urea-induced folding/unfolding reactions at pH 4.2, including one that accumulates with a time constant of ~30 μs during refolding at low urea concentrations, and a second one formed within ~200 μs of unfolding at high urea concentrations. Assuming that the pH 4 intermediate of sw-apoMb corresponds to the M_eq of this study, the counterpart of the burst phase intermediate, I, would be the sw-apoMb refolding intermediate. Indeed, even at pH 4.2 the sw-apoMb refolding intermediate accumulated in the 100-μs range (comparable to the dead-time of the CF device used in this study), which would be observed as the burst phase intermediate during refolding under native conditions at pH 6.0. On the other hand, there is a distinct difference in the fluorescence properties between these two intermediates. The I state of h-apoMb is less fluorescent than U, whereas the sw-apoMb folding intermediate exhibits a higher fluorescence intensity compared to U. Nevertheless, because fluorescence properties often reflect the local as well as global environment around Trp residues, the sw-apoMb refolding intermediate is still likely to correspond to I based on the similarity in their kinetic behavior. In addition, it should be noted that preliminary CF unfolding measurements initiated at 0.8 M urea and pH 6.0, where M is populated, detected changes in fluorescence within the dead-time of the device, and that unfolding was much faster than the reverse I → M conversion (~10⁴ s^-1). The non-two-state behavior implies transient accumulation of an unfolding intermediate, which is consistent with the observation of the unfolding intermediate of sw-apoMb, although further investigation is required.

In summary, we systematically investigated the urea-dependence of the refolding/unfolding kinetics and unfolding equilibrium of h-apoMb, and found that five species (U, I, M, N', and N) are associated with the refolding/unfolding reactions. We quantitatively modeled the data using a five-state sequential kinetic model. The formation of M is observed over a wider range of urea concentrations (0–2.2 M) than the formation of N (0–1.6 M). Based on the differences between the urea-dependent stability of M and N, we determined that M and M_eq are formed by overcoming a shared kinetic barrier in the folding reaction and that the stability of N relative to M determines whether M transiently accumulates during folding or is populated as M_eq. An additional intermediate, I, accumulated within the dead-time of refolding, and the native-like unfolding intermediate, N', accumulated in <1 ms of unfolding.