Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases

Abstract

Several neurodegenerative diseases are linked to expanded repeats of glutamine residues, which lead to the formation of amyloid fibrils and neuronal death. The length of the repeats correlates with the onset of Huntington's disease, such that healthy individuals have <38 residues and individuals with >38 repeats exhibit symptoms. Because it is difficult to obtain atomic-resolution structural information for poly(l-glutamine) (polyQ) in aqueous solution experimentally, we performed molecular dynamics simulations to investigate the conformational behavior of this homopolymer. In simulations of 20-, 40-, and 80-mer polyQ, we observed the formation of the "alpha-extended chain" conformation, which is characterized by alternating residues in the alpha(L) and alpha(R) conformations to yield a sheet. The structural transition from disordered random-coil conformations to the alpha-extended chain conformation exhibits modest length and temperature dependence, in agreement with the experimental observation that aggregation depends on length and temperature. We propose that fibril formation in polyQ may occur through an alpha-sheet structure, which was proposed by Pauling and Corey. Also, we propose an atomic-resolution model of how the inhibitory peptide QBP1 (polyQ-binding peptide 1) may bind to polyQ in an alpha-extended chain conformation to inhibit fibril formation.

Fig. 1.

Four random-coil conformations. The simulations of polyQ 20-, 40-, and 80-mer were started from the idealized P_II conformation, and the most prevalent sampled conformations are shown.

Fig. 2.

Distribution of α-extended chain lengths in polyQ. The population and distribution of α-extended chain segment lengths over the 0- to 20-ns period. (A) Total number of counts for each simulation. (B) Breakdown of segment lengths in simulations at 3°C. (C) Simulations at 50°C. Our nonamyloidogenic control CI2 had seven counts for the same time interval and could not be seen on the graph, so it was omitted. A residue was defined to be this conformation if it was within ±30° of the average (ϕ, ψ) angles, as determined in earlier TTR simulations (7), as follows: (ϕ⁺, ψ⁺) = (45 ± 8°, 92 ± 28°) and (ϕ^-, ψ^-) = (-87 ± 7°, -49 ± 4°). Repeating α-extended chain structure was calculated by requiring that at least four sequential residues have (ϕ, ψ) angles alternating between the α_R and the α_L conformations. (D) Snapshots from 80-mer simulation at 50°C. Note the stretches along the structures with aligned carbonyl oxygens in red. A hydrogen bonded α-hairpin is evident at 15 ns, and further folding and collapse result in the structure at 20 ns. The hairpin is shown on the bottom left of the 20-ns structure, and it comes out of the plane slightly. The starting structure is not shown because of its size; it is 231 Å in end-to-end length. For comparison, the extended 5-ns structure is 121 Å in end-to-end length. Ribbon diagrams at the right show the topology of the sheet-like structure formed by the polyQ 80-mer and the converted, scrapie-like form of the prion protein (PrP^Sc) obtained in MD simulations at low pH (42, 43).

Fig. 3.

Formation of an α-hairpin from a type I turn. (A) Structural transition from type I turn to an α-hairpin. Shown is the D₂Q₁₅K₂ peptide under amyloidogenic conditions at 50°C. The conformation of each turn residue is given. The last structure shown is a representative 4:4 α-hairpin with regular hydrogen bonding. (B) Five different turns from the β-hairpin library (19).

Fig. 4.

Model of the QBP1 peptide-40-mer polyQ complex. Shown are the initial minimized conformation of the docked complex (upper) and the conformation after 10 ns (lower). The most populated hydrogen bonds during the simulation are shown in magenta, and less populated hydrogen bonds are shown in light blue. Near each hydrogen bond, the percentage of the time that the hydrogen bond was intact at 6-10 ns is given. Steric clashes with the side chain of the Pro residue in the QBP1 peptide (red dashed lines) discourage another polyQ chain from hydrogen bonding to the carbonyl face of the QBP1-polyQ complex, directly inhibiting elongation of the α-sheet.