Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein

Abstract

The aggregation of the copper-zinc superoxide dismutase (SOD1) protein is linked to familial amyotrophic lateral sclerosis, a progressive neurodegenerative disease. A recent experimental study has shown that the (147)GVIGIAQ(153) SOD1 C-terminal segment not only forms amyloid fibrils in isolation but also accelerates the aggregation of full-length SOD1, while substitution of isoleucine at site 149 by proline blocks its fibril formation. Amyloid formation is a nucleation-polymerization process. In this study, we investigated the oligomerization and the nucleus structure of this heptapeptide. By performing extensive replica-exchange molecular dynamics (REMD) simulations and conventional MD simulations, we found that the GVIGIAQ hexamers can adopt highly ordered bilayer β-sheets and β-barrels. In contrast, substitution of I149 by proline significantly reduces the β-sheet probability and results in the disappearance of bilayer β-sheet structures and the increase of disordered hexamers. We identified mixed parallel-antiparallel bilayer β-sheets in both REMD and conventional MD simulations and provided the conformational transition from the experimentally observed parallel bilayer sheets to the mixed parallel-antiparallel bilayer β-sheets. Our simulations suggest that the critical nucleus consists of six peptide chains and two additional peptide chains strongly stabilize this critical nucleus. The stabilized octamer is able to recruit additional random peptides into the β-sheet. Therefore, our simulations provide insights into the critical nucleus formation and the smallest stable nucleus of the (147)GVIGIAQ(153) peptide.

Keywords: Replica exchange method; bilayer β-sheet; free energy landscape; molecular dynamics simulations; nucleus; oligomers.

Figure 1.

Calculated secondary structure probability in the REMD runs during 100−200 ns for wild-type and I149P mutant systems at 310 K for (a) average secondary structures of all residues and residue-based (b) β-sheet, (c) coil, (d) β-bridge, and (e) bend conformations.

Figure 2.

Probability of different sizes of β-sheet (a) and the probability of the angle between two adjacent β-strands in all sizes of β-sheet in wild-type and I149P hexamers at 310 K from the REMD simulations.

Figure 3.

Representative conformations of the first nine most-populated clusters for wild-type (a) and I149P mutant (b) hexamers at 310 K from the REMD simulations. The corresponding population of each cluster is given in parentheses.

Figure 4.

Free-energy landscape (kcal/mol) for wild-type (a) and I149P (b) hexamers at 310 K from the REMD simulations, plotted as a function of the number of interpeptide H-bonds and R_g.

Figure 5.

Representative structures of bilayer β-sheets and β-barrels of wild-type (a) and I149P mutant (b) hexamers at 310 K from the REMD simulations, shown in two different views: side view and top view. Different sizes of bilayer β-sheets are denoted by m + n, where m and n represent, respectively, the m- and n-stranded β-sheets forming the bilayer β-sheets. The four different β-barrels include four-, five-, and six-stranded open β-barrels (open B4, open B5, open B6) and six-stranded closed β-barrel (closed B6).

Figure 6.

Side-chain−side-chain contact probability map (a,b) and main chain H-bond number (c,d) averaged over all 100−200 ns REMD-generated conformations at 310 K for wild-type and I149P hexamers.

Figure 7.

Analysis of the structural stability of 3 + 3 bilayer β-sheet for fibril-like wild-type and I149P mutant hexamers: time evolution of Cα-RMSD in conventional MD simulations with respect to the 3 + 3 bilayer β-sheet at t = 0 ns (a, b) and snapshots at five different time points for (c) wild-type and (d) I149P hexamers.

Figure 8.

Time evolution of Cα-RMSD of wild-type 3 + 3 parallel bilayer β-sheet hexamer in conventional MD simulations with respect to the center structure of three ordered clusters generated in the REMD run of wild-type hexamers. The inset is the snapshot of the center structure of cluster-25 (a), cluster-51 (b), and cluster-81 (c).

Figure 9.

Analysis of the structural stability of the 4 + 4 fibril-like parallel bilayer β-sheet of GVIGIAQ peptide in conventional MD simulations: time evolution of Cα-RMSD with respect to the 4 + 4 bilayer β-sheet at t = 0 ns (a) and snapshots at four different time points (b).

Figure 10.

Analysis of the MD trajectory on the system consisting of a 3 + 3 bilayer β-sheet and two random chains in conventional MD simulations. Time evolution of (a) the backbone H-bond number and the main-chain distance between chain 1 and chain 2. (b) The main chain center-of-mass distance between chain 1 + 2 and the upper layer β-sheet of the 3 + 3 bilayer β-sheet. (c) Representative snapshots at 12 different time points.

Figure 11.

Analysis of the MD simulation on the system consisting of a 4 + 4 bilayer β-sheet and two random chains in conventional MD simulations. The time evolution of (a) backbone H-bond number, the minimum distance between chain 1 and 4 + 4 bilayer β-sheet, and the main-chain distance between chain 1 and chain 2. (b) Backbone H-bond number and the minimum distance between chain 2 and chain 8. (c) Representative snapshots at 12 different time points.