Comparative molecular dynamics simulations of pathogenic and non-pathogenic huntingtin protein monomers and dimers

Abstract

Polyglutamine expansion at the N-terminus of the huntingtin protein exon 1 (Htt-ex1) is closely associated with a number of neurodegenerative diseases, which result from the aggregation of the increased polyQ repeat. However, the underlying structures and aggregation mechanism are still poorly understood. We performed microsecond-long all-atom molecular dynamics simulations to study the folding and dimerization of Htt-ex1 (about 100 residues) with non-pathogenic and pathogenic polyQ lengths, and uncovered substantial differences. The non-pathogenic monomer adopts a long α-helix that includes most of the polyQ residues, which forms the interaction interface for dimerization, and a PPII-turn-PPII motif in the proline-rich region. In the pathogenic monomer, the polyQ region is disordered, leading to compact structures with many intra-protein interactions and the formation of short β-sheets. Dimerization can proceed via different modes, where those involving the N-terminal headpiece bury more hydrophobic residues and are thus more stable. Moreover, in the pathogenic Htt-ex1 dimers the proline-rich region interacts with the polyQ region, which slows the formation of β-sheets.

Keywords: aggregation; huntingtin; molecular dynamics; oligomer; polyglutamine.

FIGURE 1

Sequence of Htt-Q₂₃ and Htt-Q₄₈ studied in this work. The Nt₁₇ region is highlighted in red, polyQ in blue, and the PRD is shown in yellow for polyP₁₁ and polyP₁₀ and rose for the other PRD parts.

FIGURE 2

Secondary structure preferences per residue of Htt-Q₂₃ (A) and Htt-Q₄₈ (B) monomers. The bars represent the additive secondary structure probabilities consisting of α-helix (gray), β-strand/bridge (cyan), and β-turn/bend (magenta). The difference to 1.0 presents the other structures, in particular PPII and random coil. Representative structures were determined from conformational clustering using an RMSD cutoff of 0.5 nm for Htt-Q₂₃ (C) and Htt-Q₄₈ (D). The population of each cluster is given. The Nt₁₇ region is shown in red, polyQ in blue, polyP₁₁ and polyP₁₀ in yellow, and the rest of the PRD in rose.

FIGURE 3

Structural properties of Htt-Q₂₃ and Htt-Q₄₈ monomers. (A) The RMSFs of the Cα atoms of Htt-Q₂₃ (left) and Htt-Q₄₈ (right). The polyQ regions are highlighted by a blue shade. (B) Intra-protein distance matrices of Htt-Q₂₃ (left) and Htt-Q₄₈ (right). The color bar on the right shows the average residue-residue distance (in nm). (C) The average SASA of the Nt₁₇ residues (with standard errors) for Htt-Q₂₃ (red) and Htt-Q₄₈ (blue). (D) The free energy surface of Htt-Q₂₃ (left) and Htt-Q₄₈ (right) was calculated using the radius of gyration and the end-to-end distance. The color bar shows the value of the free energy (ΔG) in kcal/mol.

FIGURE 4

Residue-residue contacts and secondary structures in Htt-Q₂₃ and Htt-Q₄₈ dimers. (A) The intra- and inter-protein contacts between residues for Htt-Q₂₃ (top) and Htt-Q₄₈ (bottom) dimers. The intra-protein contacts within protein 1 are shown below the main diagonal and within protein 2 above the main diagonal. The color bar on the right shows the average distances (in nm). (B) The time- and protein-averaged probability of secondary structure per residue for Htt-Q₂₃ (top) and Htt-Q₄₈ (bottom) dimers. The bars represent the additive secondary structure probabilities consisting of α-helix (gray), β-strand/bridge (cyan), and β-turn/bend (magenta). The difference to 1.0 presents the other structures, in particular PPII and random coil.

FIGURE 5

Structures and SASAs of dimers. The four most populated cluster structures for the Htt-Q₂₃ (A) and Htt-Q₄₈ (B) dimer. The proteins are shown as cartoons and colored red for the negatively charged residues, blue for the positively charged ones, and white otherwise. The side chains at the protein interfaces are shown as sticks. (C) The distribution of the hydrophobic (right) and polar (left) SASAs of the four most populated clusters for Htt-Q₂₃ (top) and Htt-Q₄₈ (bottom) dimers are shown. The results for the four clusters are shown in different colors according to the color mapping on the right.