1. Introduction
In general, the biological functions of proteins require the correct folding and sufficient stability. However, protein stability is strongly influenced by the type of solvent, ionic strength, and protein concentration. Protein folding is the process by which a peptide chain assumes its functional shape or conformation. All protein molecules are heterogeneous unbranched chains of amino acids. By coiling and folding into a specific three-dimensional (3D) shape, they can perform their biological functions. The reversal of this process is known as denaturation, whereby a native protein loses its functional conformation and becomes an amorphous and non-functional amino acid chain [
1]. Studying the structural dynamics of denatured proteins can provide insights into the physical and chemical principles that govern protein folding. The unfolded state is frequently viewed as unstructured and featureless and is thus described as a random-coil [
2]. To fully understand the conformational behavior of a protein, it is necessary to define not only the structure of its native state but also those of various denatured states [
3,
4]. Recent studies have revealed the biological significance of denatured states in processes such as aggregation [
5,
6,
7], chaperone binding [
8,
9], and membrane transport [
10,
11]. A variety of denatured states have also been identified that differ in their overall dimensions and the extent of residual secondary and tertiary structures [
12,
13,
14]. In particular, recent studies have shown that heat- and chemical-denatured hen egg-white lysozyme (HEWL) increased the antibacterial activity against Gram-negative bacteria, representing a novel candidate antimicrobial agent [
15,
16].
Urea is one of the most widely used chemical denaturing agents; it is used to understand the relationship between the structure and enzymatic function of proteins, as well as their conformational stability. It is known that urea increases the solubility of nonpolar molecules in water and prevents the formation of micelles. This effect is substantially more pronounced with regard to proteins [
1]; urea acts both directly, by improving the solubility of hydrophobic residues, and indirectly, by disrupting the aqueous network structure that forms around the native protein [
17,
18]. Therefore, when the urea concentration increases, the protein increasingly loses its compact shape in favor of a flexible structure.
Porcine pepsin (molecular weight: 34.55 kDa) is a gastric aspartic proteinase that has been the subject of extensive study; pepsin is known to play an integral role in the digestive process of many vertebrates [
19,
20]. X-ray crystallography studies have shown that porcine pepsin consists of two structurally homologous domains, an N-terminal domain (residues 1–172), and a C-terminal domain (residues 173–326), and that its active binding site is located in the cleft between the domains; the secondary structures of these domains were found to consist almost entirely of β-sheets [
19,
20,
21]. For pepsin to be activated, the catalytic site requires two aspartate residues, Asp32 and Asp215, one of which has to be protonated, and the other deprotonated [
22]. The activation of these residues has been found to occur over a pH range of 1–5 [
19,
23]. Pepsin undergoes a conformational transition from a native (at acidic pH) to a denatured (at alkaline pH) state over a narrow pH range (between 6 and 7) [
24,
25,
26,
27]. The denaturation of porcine pepsin as a function of pH and temperature has been extensively studied in terms of its secondary structure and enzymatic activity using a variety of spectroscopic methods [
24,
25,
26,
27,
28,
29,
30]. We previously studied the structure of porcine pepsin at various pH values in terms of their size and shape using small-angle X-ray scattering (SAXS) [
31]. However, in order to obtain a detailed picture of its 3D structure and conformational stability, the analysis of the effect of the denaturing agent urea on the structure and enzymatic activity of pepsin is necessary.
While macromolecular X-ray crystallography and nuclear magnetic resonance (NMR) are yielding exponentially growing data on native protein structures, a relatively limited number of biophysical techniques can provide information on the denatured state that is defined as unstructured [
2].
SAXS is a powerful method for the structural characterization of both ordered and disordered proteins in solution. It provides information regarding the sizes and shapes of proteins and complexes over a broad range of molecular sizes ranging from several kDa to GDa [
32,
33,
34]. In particular, SAXS can comprehensively characterize dynamic processes in systems where macromolecular structures are evolving under varying experimental conditions (e.g., time, pH, pressure, or different reagents) [
35,
36,
37,
38]. In general, a highly purified monodisperse ideal sample without intermolecular interactions is essential for the reconstruction of 3D models from SAXS data. However, no additional labeling, crystallization, freezing, or chemical modification of the sample is needed, which makes SAXS universally applicable. SAXS is particularly suitable for studying flexible and disordered proteins, large biomolecular assemblies and oligomeric mixtures, and enzyme kinetics, which are difficult to investigate using other structural biology methods [
35].
In this study, to obtain more information on the 3D structure of porcine pepsin and its conformational stability, and because of the importance of establishing the relationship between the structure and enzymatic activity of proteins, we investigated the effect of the denaturing agent urea on the structure of porcine pepsin using Raman spectroscopy and SAXS.
3. Results and Discussion
Prior to MALS and SAXS measurements, the purity of the pepsin samples was confirmed using 13% acrylamide separation gel, and bands were visualized using Coomassie brilliant blue R-250 staining reagent.
Figure 1a shows the SDS-PAGE electropherogram of the pepsin molecules in the buffer solution in the absence of urea. As shown in
Figure 1a, one strong band was observed at the 35–40 kDa marker, which is close to the theoretical molecular weight of pepsin (34.5 kDa). To corroborate this result and investigate the monodispersity of pepsin in the buffer solution in more detail, AF4-MALS measurement was performed.
Figure 1b shows the AF4-MALS profile of pepsin in the buffer solution in the absence of urea; we observed a single distinct peak with no other oligomers or aggregates. The molecular mass of pepsin protein was estimated to be approximately 38.3 kDa, similar to its theoretical molecular mass (34.5 kDa). This result indicates that the pepsin molecules were present in a monodisperse, monomeric conformational state in terms of both overall size and molecular mass in solution.
To understand the structural changes in pepsin at the secondary structure level at various concentrations of the denaturing agent urea in aqueous media, Raman measurements were performed using a dispersive Raman spectrometer. The Raman spectra of the film and solution states of pepsin were distinct in terms of both peak position and broadness (data not shown). These Raman spectra showed not only intra-molecular information such as peptide secondary structure, but also peptide-environment interactions such as those between the peptide and the buffer solution and between the peptide and the denaturing agent. We observed representative Raman bands that indicated conformational changes in pepsin in aqueous media known as the amide I (1600–1800 cm
−1) and amide III (1230–1400 cm
−1) bands [
48,
49]. The amide I band (C=O stretch vibration) is most often characterized to clarify the secondary structures of proteins in solution, such as α-helix, β-sheet, and random-coiled conformations. However, in this region, detailed structural analysis was limited because of the strong Raman signals caused by the C=O vibrations of sodium acetate and urea in the buffer solution used in this study (data not shown). The spectral range of the amide III bands (H–N–C bending vibration) is suitable for observations without strong interference by unexpected Raman scattering. The amide III bands are also considered to be markers of secondary structures such as helices (260–1400 cm
−1), β-sheets (1230–1240 cm
−1), and random-coils (1240–1260 cm
−1) [
48,
49,
50,
51].
Figure 2a shows the Raman spectra of pepsin in solution with the amide III bands as a function of urea concentration. A broad Raman band of approximately 1250 cm
−1 could be classified into two types: β-sheet and random-coil conformations at 1231 cm
−1 and 1246 cm
−1, respectively. The intensity of the β-sheet band appeared to decrease gradually at 6–10 M urea when compared to those at 0–5 M urea. Conversely, there were no significant differences in the intensity of the random-coil band over the urea concentration range of 0–10 M. The amide III band, which is related to helical conformations, was prominent at 1341 and 1358 cm
−1 and showed much more discrete double-peak patterns than those measured at 1231 and 1246 cm
−1. It was also found that the Raman scattering patterns of pepsin molecules at 0–5 M urea were different from those measured at 6–10 M urea, similar to that observed for the amide III band at 1231 cm
−1. For quantitative analysis, we attempted to calculate the integrated area of the amide III band at 1320–1370 cm
−1.
Figure 2b exhibits the integrated area of the band corresponding to the helical conformation as a function of urea concentration, and clearly shows that the value of integrated area of about 600 for pepsin at 0–5 M urea abruptly decreased to 350–400 at 6–7 M urea, and to approximately 300 at 8–10 M urea. Considering the Raman spectral data above, it can be predicted that pepsin molecules exist in a fully folded state at 0–5 M urea, are partially unfolded at 6–7 M urea and exist in a highly unfolded state at 8–10 M urea in terms of secondary structure. These results are similar to those of the unfolding process of pepsin as a function of the pH reported previously [
30,
39].
In order to investigate the effect of urea on the structural stability of pepsin, and to confirm the results of Raman analysis above, synchrotron SAXS measurements were performed at room temperature with 0–10 M urea. Our SAXS experimental results show that the pepsin structures formed during the initial incubation period are stable for 2 days, until the end of the SAXS experiment. In terms of structural stability, the 3D structure of pepsin before and after chemical denaturation as a function of urea concentration was studied quantitatively. The effect of urea concentration on the experimental X-ray scattering profiles of pepsin at pH 4.5 is shown in
Figure 3. Overall, it appeared that the scattering profiles of the GASBOR ab initio envelope reasonably fit the experimental data for pepsin exposed to 0–10 M urea. We found that the experimental data for pepsin in the absence of urea were consistent with those calculated based on monomeric crystal structure of pepsin, indicating that pepsin without urea showed a very similar conformation to that observed in its crystal structure and that the absence of interparticle interference in our experimental conditions. Besides, there were also some similarities in the scattering patterns at 0–6 M urea. We recognized that as the urea concentration increased above 6 M to 10 M, the scattering patterns increasingly deviated from those measured at 0–6 M urea. This indicates that pepsin at 7–10 M urea underwent significant conformational changes, shifting from a globular form to a fully unfolded conformation due to urea-induced denaturation.
As the classical and most widely used structural parameter obtained from the SAXS data, the radius of gyration (
Rg) provides a measure of the overall size of biological macromolecules in solution [
52]. The
Rg can be defined as the average electron-density-weighted, root-mean-squared distance of the scatters from the center of density in the molecule [
52]. The
Rg value is smaller for proteins with a compact, globular state than for those with a partially and/or fully unfolded state, even though they have an equal number of amino acid residues [
52]. The
Rg can be calculated using the Guinier approximation using a small-angle region for
qRg < 1.3 (hereafter, the radius of gyration obtained from the Guinier approximation is referred to as
Rg,G). Guinier plots of ln[
I(
q)] versus
q2 of the scattering profiles of pepsin in solution at 0–10 M urea are displayed in
Figure 4a,b. The scattering profiles plotted as ln[
I(
q)] vs.
q2 showed linearity in the small
q2 region. The
Rg,G values of pepsin at different urea concentrations were determined based on the slope of the linear fit. The radius of gyration as a function of urea concentration was plotted, as shown in
Figure 4c. In addition, we attempted to calculate pepsin molecular mass
MMSAXS from the SAXS intensity extrapolated to
q = 0,
I(0), the protein volume V (in Å) obtained from the invariant
Q, and the average protein density of ρ
m = 0.83 × 10
−3 kDa Å
−3 [
43]. Our data show that pepsin molecules exist in monomeric form in solution over a wide range of denaturant urea concentrations (0–10 M), despite some variations in MM values. The determined
Rg,G and
MM values are also listed in
Table 1. The radius of gyration of pepsin in solution in the absence of urea was estimated to be 22.08 ± 0.22 Å, which almost exactly corresponded to that (21.34 ± 0.01 Å) of the crystal structure of monomeric pepsin (PDB:3PEP). The
Rg,G values of pepsin at 0–6 M urea showed no significant differences, despite some variations in size. At concentrations of above 6 M urea, the
Rg,G value increased significantly. Based on the resulting
Rg,G values (
Figure 4c and
Table 1), we found that the onset urea concentration at which
Rg,G begins to change significantly is approximately 7 M. The
Rg,G value of pepsin at 7 M urea was 23.07 ± 0.79 Å, slightly larger than those measured at 0–6 M urea. The
Rg,G values for pepsin at 8 and 9 M urea were estimated to be 32.66 ± 1.61 Å and 41.54 ± 3.43 Å, respectively, while that at 10 M urea was determined to be 50.01 ± 5.08 Å, the largest of all the measured
Rg,G values. This result was considered to be due to complete unfolding as a consequence of the collapse of the secondary and tertiary structures. Fully unfolded proteins, because of their highly extended conformations, are characterized by a larger measured average size than globular proteins with tightly well-packed core domains [
47,
52]. Our comparison of the experimentally determined
Rg,G value with that calculated from the theoretical models was used to characterize the unstructured nature of the protein. The predicted
Rg value for the unstructured conformation of pepsin was directly calculated based on the number of amino acid residues using Flory’s equation [
53]:
where
N is the number of amino acid residues,
R0 is a constant that depends on the persistence length of the peptide chain, and
ν is an exponential scaling factor; for chemically denatured proteins we used the values
R0 = 2.54 ± 0.01 and
ν = 0.522 ± 0.01. The theoretically calculated
Rg value, based on the fully unfolded state of pepsin with 326 amino acid residues, was estimated to be approximately 52.09 Å, which is consistent with that measured at 10 M urea (50.01 ± 5.08 Å). Through this observation, it was found that pepsin molecules exposed to 10 M urea have a fully extended, randomly coiled conformation in solution, owing to the complete destruction of the tightly well-packed core (sub)domain.
Generally, Kratky plots (
q2I(
q) as a function of
q) are employed to qualitatively identify the denatured states of proteins in various denatured conditions and to distinguish them from their globular conformations; the Kratky plot can discriminate specific features of the scattering profiles of pepsin between its globular and fully unfolded conformations at different urea concentrations [
52]. Typically, the scattering intensity from a solid body decays at high
q values, with values of
I(
q) ~ 1/
q4 with a bell-shaped pattern in the Kratky plot. Conversely, an ideal Gaussian chain has a 1/
q2 asymptotic of
I(
q) and displays a plateau at larger
q values. For an extended thin chain, the Kratky plot also presents a plateau over a specific range of
q, which is followed by a monotonic increase [
52].
Figure 5 shows the Kratky plots of SAXS data of pepsin at 0–10 M urea. At 0–5 M urea, we observed a distinct bell-shaped curve with a peak maximum at
q = 0.08 in the small
q region (
q < 0.15). This distinct symmetrical peak pattern indicates that pepsin at 0–5 M urea had a compact, globular conformation, as expected. At 6 M urea, the Kratky plot also showed a distinct peak pattern at around
q = 0.08 but was slightly asymmetrical compared to those at 0–5 M urea. This observation implies that pepsin underwent a weak urea-induced denaturation process at 6 M, though the overall size remained unchanged. At 7 M urea, the Kratky plot exhibited a weak peak maximum at around
q = 0.1, with a shift toward high
q region; the symmetrical or asymmetrical peak pattern observed at 0–6 M almost entirely disappeared. This result may have been because of the highly extended conformation due to the denaturation of the compact, globular pepsin structure. At 8–10 M urea, the Kratky plots showed an interesting scattering feature that differed markedly from those obtained at other urea concentrations. The peak maximum in the small
q region was not present in the Kratky plot; the plot rose rapidly in the small
q region and then increased gradually in the intermediate and high
q regions. This pattern is typical of the Kratky-Porod chain [
54], indicating that the secondary and tertiary structures of pepsin were almost completely destroyed at high urea concentrations, leading to a randomly coiled conformation.
In real space, the particle sample can be conveniently described using the distance distribution function
p(
r), which is a histogram of the distances between all possible pairs of atoms within a particle [
52]. The
p(
r) function can be obtained from experimental scattering data using indirect Fourier transformation [
55,
56]. In some cases, it is more intuitive to interpret the structural properties rather than the scattering data itself. In particular, for compact globular particles, the
p(
r) shows a symmetrical bell-shaped pattern, whereas, for unfolded particles, it has an extended tail [
52]. The radius of gyration can be calculated from the
p(
r) function (hereafter, referred to as
Rg,p(r)), which often provides a more reliable estimate than the Guinier approximation, especially in unstructured systems [
57].
Figure 6a,b show the
p(
r) function for pepsin incubated with various urea concentrations based on an analysis of the experimental scattering data using indirect Fourier transformation. The areas under the curves were normalized to 1 for ease of comparison. The function provided the radius of gyration (
Rg,p(r)), which is based on the full scattering curve, as well as the maximum dimension (
Dmax) of pepsin as the distance where the
p(
r) function approaches zero. The
Rg,p(r) and
Dmax values obtained are summarized in
Table 1. In addition, for an improved understanding of these size changes, the
p(
r) function-based radius of gyration and maximum dimension values as a function of urea concentration is plotted in
Figure 6c. Overall, the resulting
Rg,p(r) values were highly consistent with those from the Guinier approximation, despite several size variations. In particular, from the resulting
Rg,p(r) values, we observed that the onset urea concentration leading to an increase in overall size is approximately 7 M, which is consistent with the estimates obtained from the Guinier approximation. We also found a relatively large difference between the
Rg,p(r) and
Rg,G values at both 9 and 10 M urea under fully denaturing conditions. Considering that the
Rg,G is estimated from the restricted
q range in the Guinier region, we expected that the
Rg,p(r) based on the full scattering profile would be more reliable for pepsin molecules in a fully unfolded state under strongly denaturing conditions. We computed a theoretical
p(
r) function for the atomic coordinates of the crystal structure of the monomeric pepsin protein (PDB code 3PEP) and compared it with those measured for pepsin at 0–10 M urea. The
p(
r) functions for pepsin at 0–6 M urea exhibited a symmetrical peak pattern, which is characteristic of a compact globular conformation, and was considerably similar to that of the crystal structure (
Rg,p(r) = 21.20 ± 0.19 Å,
Dmax = 67.0 Å) of pepsin. However, the
p(
r) functions for pepsin at 7–10 M urea clearly revealed an asymmetric form, with the maximum dimensions shifted toward the long-distance region compared to those measured at 0–6 M. The
Dmax value increased in the following order: 7 M urea (117.0 Å) < 8 M urea (129.0 Å) < 9 M urea (197.0 Å) ≤ 10 M urea (198.0 Å), indicating that the conformation of pepsin deviated considerably at increased urea concentrations higher than 6 M.
The correlations between the Kratky plot analysis, the
p(
r) function analysis, and the molecular structure were further examined by reconstructing ab initio structural models from the X-ray scattering data using GASBOR. To improve the reliability of the final solution models, multiple runs of GASBOR were used, and the most probable models among them were selected.
Figure 7 shows the structural models reconstructed for pepsin in solution at 0–10 M urea. As described in the
p(
r) function analysis, the structural model for pepsin at 0 M urea appeared to be close to that of the monomeric crystal structure in terms of overall shape and dimension. The structural models for pepsin at 1–5 M urea showed a compact globular conformation, similar in overall shape to that at 0 M urea. At 6 M urea, the structural model showed a bent conformation along the horizontal axis in the central region between N- and C-terminal domains, slightly different to those at 0–5 M urea, but showing minimal differences in size.
It is interesting to note that based on the Kratky plot in
Figure 5, pepsin should be present in a partially denatured and compact globular conformational state at 6 M urea. According to this solution model, we identified an intermediate pepsin conformation that was dominant during an early stage of denaturation. Furthermore, such a subtle conformational change may provide clues regarding the reduced enzymatic activity of pepsin under denaturing conditions, taking into account the activity result reported previously [
58]. The structural model for pepsin at 7 M urea revealed a highly extended and linear conformation along the vertical axis. These results were consistent with the Kratky plot and
p(
r) function analyses results, which showed that pepsin at 7 M urea is present in a highly unfolded and extended conformational state. Similarly, the structural model at 8 M urea was more extended than that at 7 M urea. The structural models for pepsin at 9 and 10 M urea adopted a fully unfolded and randomly coiled conformation that was significantly extended along the vertical axis, as confirmed by the results of the Kratky plot and
p(
r) function analyses. However, it was suspected that pepsin molecules at high urea concentrations might coexist in multiple conformations with conformational polydispersity under highly denatured conditions.
Therefore, to confirm that the GASBOR-derived reconstructed model for pepsin at 10 M urea was a representative and reliable solution model for any interpretations presented, we attempted to generate an ensemble of possible conformations of pepsin and select a subset of conformations that best fit the experimental data for pepsin at 10 M urea, with a random sequence designation, using the EOM program (
Figure 8). Interestingly, it was found that the EOM-derived subset of conformations showed randomly coiled conformations similar in overall shape to the GASBOR-derived dummy residue model for pepsin under the same conditions (
Figure 9). Therefore, the GASBOR ab initio structural models for pepsin at high urea concentrations were confirmed to be trustworthy solution models that appropriately represented the fully unfolded conformations of pepsin under highly denatured conditions. Besides, we observed that pepsin was present in soluble submicron aggregates without precipitation when the pepsin solution, including 10 M urea, was diluted 10-fold (1 M) with a buffer solution in the absence of urea (data not shown). Collectively, from these results, we observed that pepsin is structurally dynamic over a wide range of urea concentrations, adopting several forms ranging from the crystal structure-like folded state to randomly coiled conformations such as the Kratky-Porod chain.