Understanding protein aggregation from the view of monomer dynamics

Abstract

Much work in recent years has been devoted to understanding the complex process of protein aggregation. This review looks at the earliest stages of aggregation, long before the formation of fibrils that are the hallmark of many aggregation-based diseases, and proposes that the first steps are controlled by the reconfiguration dynamics of the monomer. When reconfiguration is much faster or much slower than bimolecular diffusion, then aggregation is slow, but when they are similar, aggregation is fast. The experimental evidence for this model is reviewed and the prospects for small molecule aggregation inhibitors to prevent disease are discussed.

Fig. 1

Kinetic models (i–iii) describing the early phases of aggregation. For all schemes, k_bi = 1 × 10⁵ s⁻¹, k_O = 100 s⁻¹ and k₁ as marked on the plots. (a) Solution to scheme (i), in which O forms by conformational change of [M*M*] and k₋₁ = k₁. (b) Solution to scheme (ii), in which O forms by the addition of a third monomer, M* to [M*M*] and k₋₁ = 0.5k₁. (c) Solution to schemes (ii) and (iii) for k_nuc = 1s⁻¹ and k_f = 100s⁻¹.

Fig. 2

Determination of the rate of contact formation between the probe, tryptophan (W), and the quencher, cysteine (C), within an unfolded protein. Pulsed optical excitation leads to population of the lowest excited triplet state of tryptophan. Tryptophan contacts cysteine in a diffusion-limited process with rate k_D+, and then either diffuses away or is quenched by the cysteine. The observed rate of Trp triplet decay is given by $k_{\text{obs}}=\frac{k_{\mathrm{D}+}q}{q+k_{\mathrm{D}-}}$ where k_D+ is the rate of diffusion of the two ends towards each other, k_D− is the rate of diffusion away and q is the rate of quenching. If q ≫ k_D−, the observed lifetime reduces to k^obs ≈ k_D+. More generally, eqn (1) can be rearranged to give $\frac{1}{k_{\text{obs}}}=\frac{1}{k_{\mathrm{D}+}}+\frac{k_{\mathrm{D}-}}{q{k}_{\mathrm{D}+}}=\frac{1}{k_{\mathrm{D}+}(\eta ,T)}+\frac{1}{k_{\mathrm{R}}\left(T\right)}$ where k_R is the reaction-limited rate and k_D+ is the diffusion-limited rate, T is the temperature and η is the viscosity of the solvent. The reaction-limited and diffusion-limited rates are given by Szabo Schulten and Schulten theory which describes the dynamics of unstructured peptides as diffusion on a one-dimensional potential of mean force that is related to the distribution (P(r)) of Trp-Cys distances r $k_{\mathrm{R}}=\underset{a}{\overset{l_c}{\int }}q\left(r\right)P\left(r\right)\mathrm{d}r$ $\frac{1}{k_{\mathrm{D}+}}=\frac{1}{k_{\mathrm{R}}2D}\underset{a}{\overset{l_c}{\int }}\frac{\mathrm{d}r}{P\left(r\right)}{\left\{\underset{r}{\overset{l_c}{\int }}(q\left(x\right)-k_{\mathrm{R}})P\left(x\right)\mathrm{d}x\right\}}^2$ where q(r) is the rate of quenching at r (which has been determined experimentally by Lapidus et al.), a is the point of closest approach (typically 4 Å), l_c is the contour length of the chain between Trp and Cys (and, hence, their maximum separation), and D is the effective intramolecular diffusion coefficient. P(r) could be given by a simple polymer model such as a wormlike chain, by an empirical distribution based on experimental measurements or by a molecular dynamics simulation. Generally, both diffusion-limited and reaction-limited rates are inversely proportional to the average chain volume and the diffusion-limited rate is directly proportional to the diffusion coefficient, $k_{\mathrm{R}}\propto \frac{1}{\langle V\rangle },k_{\mathrm{D}+}\propto \frac{D}{\langle V\rangle }$

Fig. 3

Measured diffusion coefficients. (a) Diffusion coefficients measured for a variety of sequences in water at 20 °C. The dark blue bars belong to the fast reconfiguration regime, red bars to the middle regime and cyan bars to the slow regime. (b) Diffusion coefficients of α-synuclein measured in various solution conditions, with the mutation A30P (red bar) and with the aggregation inhibitor, curcumin (cyan bar). The numbers in parenthesis indicate the position within the sequence of Trp (39 or 94) and Cys (69).