The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

Abstract

Understanding the early steps of aggregation at atomic detail might be crucial for the rational design of therapeutics preventing diseases associated with amyloid deposits. In this paper, aggregation of the heptapeptide GNNQQNY, from the N-terminal prion-determining domain of the yeast protein Sup35, was studied by 20 molecular dynamics runs for a total simulation time of 20 micros. The simulations generate in-register parallel packing of GNNQQNY beta-strands that is consistent with x-ray diffraction and Fourier transform infrared data. The statistically preferred aggregation pathway does not correspond to a purely downhill profile of the energy surface because of the presence of enthalpic barriers that originate from out-of-register interactions. The parallel beta-sheet arrangement is favored over the antiparallel because of side-chain contacts; in particular, stacking interactions of the tyrosine rings and hydrogen bonds between amide groups. No ordered aggregation was found in control simulations with the mutant sequence SQNGNQQRG in accord with experimental data and the strong sequence dependence of aggregation.

Figure 1

(Upper) Time dependence of the fraction of in-register parallel contacts Q_p and in-register antiparallel contacts Q_a for one trajectory of the GNNQQNY peptide. Aggregation events to IP3, IM3, and IA3 are shown in blue, cyan, and yellow, respectively. (Lower) Projection of the aggregation events onto the free-energy surface (for the construction of the free-energy surface, see the text and the caption of Fig. 2).

Figure 2

Free energy (ΔG, Upper) and average effective energy (〈E〉, Lower) surface at 330 K as a function of the fraction of in-register parallel, Q_p, and in-register antiparallel, Q_a, contacts. A total of 10⁶ conformations sampled during the 20 simulations at 330 K were used. 〈E〉 was evaluated by averaging the effective energy values of the conformations within a bin without minimizing them. ΔG was computed as −k_BT ln(N_n,m/N_0,0), where N_n,m denotes the number of conformations with n parallel and m antiparallel contacts. The error in ΔG is estimated by separating the 20 simulations into two sets of 10 simulations each. The average error of 〈E〉 is 1.2 kcal/mol, and the average error of ΔG is 0.2 kcal/mol. Representative conformations of IP3, IM3, and IA3 sampled along the MD trajectories are shown in blue, cyan, and yellow, respectively.

Figure 3

Sum of van der Waals and electrostatic energies for the atoms in the backbone (Left) and in the side chains (Right) as a function of the fraction of in-register parallel, Q_p, and in-register antiparallel, Q_a, contacts. For clarity reasons, this plot has been rotated by 180° around a vertical axis with respect to Fig. 2.