The origins of formation of an intermediate state involved in amyloid formation and ways to prevent it are illustrated with the example of the Formin binding protein 28 (FBP28) WW domain, which folds with biphasic kinetics. Molecular dynamics of protein folding trajectories are used to examine local and global motions and the time dependence of formation of contacts between
Cαs and
Cβs of selected pairs of residues. Focus is placed on the WT FBP28 WW domain and its six mutants (L26D, L26E, L26W, E27Y, T29D, and T29Y), which have structures that are determined by high-resolution NMR spectroscopy. The origins of formation of an intermediate state are elucidated, viz. as formation of hairpin 1 by a hydrophobic collapse mechanism causing significant delay of formation of both hairpins, especially hairpin 2, which facilitates the emergence of an intermediate state. It seems that three-state folding is a major folding scenario for all six mutants and WT. Additionally, two-state and downhill folding scenarios were identified in ∼15% of the folding trajectories for L26D and L26W, in which both hairpins are formed by the Matheson–Scheraga mechanism much faster than in three-state folding. These results indicate that formation of hairpins connecting two antiparallel β-strands determines overall folding. The correlations between the local and global motions identified for all folding trajectories lead to the identification of the residues making the main contributions in the formation of the intermediate state. The presented findings may provide an understanding of protein folding intermediates in general and lead to a procedure for their prevention.An intermediate state in protein folding is involved in amyloid fibril formation, which is responsible for a number of neurodegenerative diseases (
1–
7). Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to surmount. Hence, it is necessary to determine the mechanism by which an intermediate state is formed. For example, one of the members of the WW domain family (
8,
9), the triple β-stranded WW domain from the Formin binding protein 28 (FBP28; Protein Data Bank ID code 1E0L) (
10) (), has been shown to fold with biphasic kinetics exhibiting intermediates during folding (
3,
5,
6,
11–
16). We address this problem here with the design of new FBP28 WW domain mutants and by examining their structural properties and folding kinetics.
Open in a separate windowFELs (kilocalories per mole) along the first two PCs with representative structures at the minima, and contributions of the principal modes (defined in
SI Materials and Methods) [
; black lines with black circles (principal mode 1) and red lines with white circles (principal mode 2)] to the MSFs along the θ- and γ-angles for the (
A–C) three-state, (
D–F) two-state, and (
G–I) downhill folding trajectories of L26D and (
J–L) the downhill folding trajectory of L26W. The black lines on the bottoms of
B,
C,
E,
F,
H,
I,
K, and
L correspond to the β-strand regions. I, intermediate; N, native; U, unfolded.
M represents percentages of the total fluctuations captured by the PCs for three-state (black line), two-state (red line), and downhill (blue line) trajectories of L26D and the downhill folding trajectory (green line; indistinguishable from the blue line) of L26W.
N represents the experimental structure of FBP28, in which the mutated residues are represented by spheres, and hairpins 1 and 2 are represented by blue and red, respectively (the purple region corresponds to the overlap of these hairpins). C, C terminus; E, glutamic acid; L, leucine; N, N terminus; T, threonine.Because of the small size, fast folding kinetics, and biological importance, the formation of intermolecular β-sheets is thought to be a crucial event in the initiation and propagation of amyloid diseases, such as Alzheimer’s disease, and spongiform encephalopathy, FBP28, and other WW domain proteins (e.g., Pin1 and FiP35) have been the subjects of extensive experimental (
4,
11,
17–
23) and theoretical (
3,
5,
6,
12–
16,
24–
27) studies. However, a folding mechanism of the FBP28 was debatable for a long time because of its complexity. There are not only discrepancies between experimental and theoretical results but also, different experiments that reveal different folding scenarios.In particular, Nguyen et al. (
11) studied the folding kinetics of the WT FBP28 and its full-size and truncated mutants by temperature denaturation and laser temperature–jump relaxation experiments. Nguyen et al. (
11) found that the folding of the WT FBP28 involves intermediates (three-state folding) below the melting temperature and that the strand-crossing hydrophobic cluster of Tyr11, Tyr19, and Trp30 residues, which were mutated, is not a likely origin of the three-state scenario; also, truncation at the C terminus and an increase of temperature can modulate the two- and three-state folding behavior. The conclusion regarding three-state folding was challenged by Ferguson et al. (
4), who observed single-exponential folding kinetics for the FBP28 by using fluorescence measurements and concluded that the biphasic kinetics observed by Nguyen et al. (
11) might be related to aggregation and rapidly forming ribbon-like fibrils at physiological temperature and pH, with morphology typical of amyloid fibrils.Our recent theoretical studies (
12–
16) of the same systems (
11) showed that (
i) folding of all of these systems involves intermediates; (
ii) the strand-crossing hydrophobic cluster of residues 11, 19, and 30 is not associated with biphasic kinetics; and (
iii) neither an increase of temperature nor truncation can alter the folding scenario. Moreover, discrepancies between experimental and theoretical results for some of these mutants caused by experimental limitations were clarified (
16).It also was found (
3,
5) that the WT FBP28 folds with biphasic kinetics attributed to independence in the slow formation of turn 2 contacts with respect to the remainder of the protein and identified a key surface-exposed hydrophobic contact (Tyr21 with Leu26) for enforcing the correct registry of the residues of turn 2. To show the importance of the surface-exposed hydrophobic contact (Tyr21 with Leu26) and the involvement of turn 2 in a slow formation phase, the L26A mutant was studied (
3). The fast phase (formation of hairpin 1) was not affected by this mutation, whereas the slow phase became even slower, which also was confirmed experimentally (
11). These results suggested that the replacement of leucine by alanine actually stabilizes the misregistered turn 2 conformations relative to the WT; hence, it was concluded (
3) that the surface-exposed hydrophobic contact (Tyr21 with Leu26) might be responsible for tying down turn 2 with a correctly formed hairpin. It should be noted that this surface-exposed hydrophobic contact is not present in other members of the WW domain family, which fold with monophasic kinetics.Later theoretical studies (
6,
12–
16) of the WT FBP28 confirmed the results of ref.
3, showing biphasic folding kinetics with a stable intermediate state. Therefore, to prevent the formation of the intermediate state, it is logical to make mutations in the region of turn 2 and the third β-strand to speed up the formation of hairpin 2 as implemented here. However, based on the results of mutant L26A (
3), it is not an easy task to ensure the elimination of intermediates and therefore, requires a detailed understanding of folding/misfolding mechanisms, folding/misfolding pathways, and effect of temperature on folding mechanism, etc., to identify proper sites for mutations.Based on previous studies (
3,
15), Leu26 is one of the main residues in which mutation might speed up the correct registry of turn 2. Moreover, the FBP28 is the only WW domain among 200 WW domain sequences that contains leucine at this position (
3). Usually, this position is almost always occupied by a charged residue or glycine; therefore, following the natural tendency of the WW domain family, two mutants were designed, replacing leucine 26 with negatively charged polar amino acids: aspartic acid and glutamic acid (L26D and L26E, respectively). Also, replacement of leucine by alanine (the smallest nonpolar aliphatic amino acid) was found to slow down the process (
3,
11); hence, for replacement of leucine 26, we also selected a very nonpolar and larger aromatic amino acid, tryptophan (L26W). It should be noted that leucine at position 26 is not a reflection of negative design by evolution but rather, is a result of pressure to maximize specificity through use of polar residues (
3). Based on earlier results on the binding affinity of the WW domain, it was proposed (
3) that requirements for ligand specificity have led to a local sequence with a strong propensity for a misregistered turn.The next mutant was made by substituting a negatively charged polar amino acid, glutamic acid 27, with a nonpolar aromatic amino acid, tyrosine (E27Y). Finally, two more mutants were designed by replacing a neutral polar amino acid, threonine 29, with a negatively charged polar amino acid, aspartic acid (T29D) and a nonpolar aromatic amino acid, tyrosine (T29Y). Both Glu27 and Thr29 are critically placed residues contributing the most to the mean-square fluctuations (MSFs) (
15), and mutation of these residues by disfavored amino acids might destabilize the misregistered turn 2 and β-strand 3 and speed up the correct registry.To characterize the effects of these mutations, the six recombinant proteins carrying a single-point mutation were expressed, and their structures were studied by high-resolution NMR spectroscopy (
SI Materials and Methods). All mutants adopt the triple-stranded antiparallel β-sheet characteristic of the WW fold, with slight variations caused by each specific mutation (
Fig. S1). The experimental and theoretical melting temperatures (
Tm values) for each mutant were determined with differential scanning calorimetry and multiplexed replica exchange molecular dynamics (MD) simulations, respectively (
Table S1). We also ran simulations consisting of 120 (for WT and L26D) and 96 (for L26E, L26W, E27Y, T29D, and T29Y) canonical MD trajectories generated with the coarse-grained united residue (UNRES) force field (
SI Materials and Methods) (
28–
30) at five and four different temperatures, respectively (24 MD trajectories, with ∼1.4 μs formal time and effectively ∼1.4 ms of each at each temperature), which were below, very close to, and above (for some mutants) the melting temperatures. The folding dynamics of each system were analyzed in terms of principal component analysis (PCA) (
SI Materials and Methods) (
12,
15,
31) describing the global motions of the protein, local motions of each residue [free-energy profiles (FEPs) along the amino acid sequence], and distances between the
Cαs and
Cβs of selected pairs of residues forming hairpins 1 and 2 over time.
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