The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation

Abstract

We have performed simulated tempering molecular dynamics simulations to study the thermodynamics of the headpiece of the Huntingtin (Htt) protein (N17(Htt)). With converged sampling, we found this peptide is highly helical, as previously proposed. Interestingly, this peptide is also found to adopt two different and seemingly stable states. The region from residue 4 (L) to residue 9 (K) has a strong helicity from our simulations, which is supported by experimental studies. However, contrary to what was initially proposed, we have found that simulations predict the most populated state as a two-helix bundle rather than a single straight helix, although a significant percentage of structures do still adopt a single linear helix. The fact that Htt aggregation is nucleation dependent infers the importance of a critical transition. It has been shown that N17(Htt) is involved in this rate-limiting step. In this study, we propose two possible mechanisms for this nucleating event stemming from the transition between two-helix bundle state and single-helix state for N17(Htt) and the experimentally observed interactions between the N17(Htt) and polyQ domains. More strikingly, an extensive hydrophobic surface area is found to be exposed to solvent in the dominant monomeric state of N17(Htt). We propose the most fundamental role played by N17(Htt) would be initializing the dimerization and pulling the polyQ chains into adequate spatial proximity for the nucleation event to proceed.

Fig 1

The two initial configurations used for simulations of the N17 headpiece: (a). A helical structure and (b). A random-coil structure.

Fig 2

(a). Amount of time the ST simulations starting from a helical structure spent at each of the 50 temperatures. (b). The same as (a) except that data is collected from simulations starting from a coil structure.

Fig 3

Convergence of the average helical properties as a function of time at 300K. Helix properties at each conformation is defined according to classical LR counting theory. Plots obtained from simulations starting from the helix structure (black, circle) and the coil structure (red, square) are displayed for (a). average helical content. (b). average number of helical segments.

Fig 4

Helical content as a function of temperature obtained from ST simulations starting from the helical structure (black) and those from the coil structure (red). Error bars are calculated by block averaging over the configurations later than 32ns.

Fig 5

Alpha helix (black), 3₁₀-helix (red) and loop (green) content by residue at 300K. There is a higher propensity for alpha for the first 10 n-terminal residues, followed by a sharp peak in loop content and a second area of high probability for alpha helix content at the C-terminus. This indicates a tendency for a 2-helix bundle, and can be visualized in figure 7.

Fig 6

(a). Alpha helix content by residue over a series of temperatures. There is a trend over all residues for helical content to decrease with increased temperature. (b) 3₁₀-helix content by residue over a series of temperatures. (c). Loop content by residue for a series of temperatures. It is interesting to note the dramatically increased fraction of loop in the two helical stretches, but the relatively low temperature dependence of residue 10.

Fig 7

Structures closest to cluster center and the population at 300K for each of the 10 clusters are shown. The most populated cluster (cluster 9) is a two-helix bundle structure.

Fig 8

Probability for different states of the system: N-terminal helix only, two-helix, one straight helix and disordered state. N-terminal helix state contains a N-terminal helix, but the C-terminal part of the peptide is disordered. Two-helix state with a two-helix bundle is the most populated state. Plots for three temperatures are shown: 300K (Black circle), 347K (Red triangle), and 592K (Green square).

Fig 9

Cartoons showing the N17^Htt-PolQ structures in two proposed mechanisms described in the text. Two representative cluster centroid structures are shown with faces paired to minimize exposed hydrophobic surface area. Each shows a model polyQ tail (cyan) which satisfies the observed N17^Htt – polyQ domain interactions. (a). N17^Htt adopts the single straight helix conformation and has the charged residues in a surface geometry which would compliment the polyQ tail's β-strand configuration. (b). N17^Htt adopts a two-helix bundle conformation. The increased flexibility in the C-terminus of the two-helix bundle creates the turn necessary for polyQ – N17^Htt interactions.