Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins

Abstract

Proteins function by interacting with other molecules, where both native and nonnative interactions play important roles. Native interactions contribute to the stability and specificity of a complex, whereas nonnative interactions mainly perturb the binding kinetics. For intrinsically disordered proteins (IDPs), which do not adopt rigid structures when being free in solution, the role of nonnative interactions may be more prominent in binding processes due to their high flexibilities. In this work, we investigated the effect of nonnative hydrophobic interactions on the coupled folding and binding processes of IDPs and its interplay with chain flexibility by conducting molecular dynamics simulations. Our results showed that the free-energy profiles became rugged, and intermediate states occurred when nonnative hydrophobic interactions were introduced. The binding rate was initially accelerated and subsequently dramatically decreased as the strength of the nonnative hydrophobic interactions increased. Both thermodynamic and kinetic analysis showed that disordered systems were more readily affected by nonnative interactions than ordered systems. Furthermore, it was demonstrated that the kinetic advantage of IDPs ("fly-casting" mechanism) was enhanced by nonnative hydrophobic interactions. The relationship between chain flexibility and protein aggregation is also discussed.

Figure 1. Free-energy profiles of the binding process.

Free-energy profiles were calculated using the fraction of native intermolecular contacts (Q _b) as a reaction coordinate for systems with different degrees of chain flexibility. (A–D)  = 0.29, 0.46, 0.65, and 0.85 by tuning the intramolecular interaction parameter α from 0.1, 1.0, 1.5 to 3.0. The two vertical dashed lines in panel (B) indicate the definition of the unbound state (U), intermediate state (I), and bound state (B). The strength of the nonnative hydrophobic interactions (K _HP) ranges from 0.00 to 1.50.

Figure 2. Thermodynamic properties of systems with different degrees of chain flexibility.

(A) Correlation between the population of the intermediate state P(I) and the strength of the nonnative hydrophobic interactions, K _HP. (B) Effect of the nonnative hydrophobic interactions on the stability of the complex which is measured by the free-energy difference between the bound state and the unbound state. (C) Effect of the nonnative hydrophobic interactions on the transition temperature T _m.

Figure 3. Properties of the free pKID domain in the presence of nonnative hydrophobic interactions.

(A) radius of gyration (R _g), (B) average number of nonnative contacts (), and (C) the average fraction of native contacts ().

Figure 4. Characterization of the number of nonnative contacts.

(A–C) The average number of nonnative contacts along the binding process when the strength of nonnative hydrophobic interactions was increased: (A–C) K _HP = 0.50, 1.00, and 1.50. (D) Correlation between the average number of nonnative contacts at the intermediate state and . K _HP was set 1.50. (E) Correlation between the average number of nonnative contacts in the bound state and . K _HP was set 1.50. (F) Correlation between and K _HP. The definitions of the intermediate state and bound state are presented in Figure 1.

Figure 5. Effect of the nonnative hydrophobic interactions on the binding kinetics.

(A) Mean first passage time (MFPT) of the binding process as a function of K _HP. (B) Correlation between the relative binding rate and K _HP. The relative binding rate was computed as . (C) Correlation between the K _HP corresponding to the maximum binding rate, K _HP ^max-rate, and . (D) A typical binding trajectory for the system with  = 0.46 under K _HP = 1.50.

Figure 6. Kinetics analysis of the binding process.

Effect of the nonnative hydrophobic interactions on (A) capture rate (k _cap), (B) evolving rate (k _evo), and (C) escape rate (k _esc) for systems with various chain flexibilities.

Figure 7. C_α distance distribution of native contacts in the pKID-KIX complex.

(A) C_α distance distribution of native contacts formed by two hydrophobic residues (triangles) and others (circles). (B) C_α distance distribution of all native contacts.

Figure 8. Effect of the nonnative contact distance on the binding kinetics.

(A) Mean first passage time (MFPT) of the binding process as a function of K _HP. (B) Correlation between the relative binding rate and K _HP. (C) Correlation between the K _HP corresponding to the maximum binding rate K _HP ^max-rate and . Contact distance σ_hϕ = 7.5 Å was used in (A–C). (D) The sensitivity of the binding rate with respect to nonnative hydrophobic interactions for σ_hϕ = 5.0 and 7.5 Å.