Conformational preferences of a 14-residue fibrillogenic peptide from acetylcholinesterase

Abstract

A 14-residue fragment from near the C-terminus of the enzyme acetylcholinesterase (AChE) is believed to have a neurotoxic/neurotrophic effect acting via an unknown pathway. While the peptide is alpha-helical in the full-length enzyme, the structure and association mechanism of the fragment are unknown. Using multiple molecular dynamics simulations, starting from a tetrameric complex of the association domain of AChE and systematically disassembled subsets that include the peptide fragment, we show that the fragment is incapable of retaining its helicity in solution. Extensive replica exchange Monte Carlo folding and unfolding simulations in implicit solvent with capped and uncapped termini failed to converge to any consistent cluster of structures, suggesting that the fragment remains largely unstructured in solution under the conditions considered. Furthermore, extended molecular dynamics simulations of two steric zipper models show that the peptide is likely to form a zipper with antiparallel sheets and that peptides with mutations known to prevent fibril formation likely do so by interfering with this packing. The results demonstrate how the local environment of a peptide can stabilize a particular conformation.

Figure 1

(A) AChE−PRAD complex with four AChE helices (blue and green) coiled around an antiparallel PRAD helix (red) (PDB entry 1VZJ). (B) Sequence of chains E−H and J from the structure. I−V is the numbering used in panel A to denote protein chains. (C) Four AChE helices without the PRAD helix. (D) One AChE helix. (E) Fourteen-residue AChE peptide extracted from an AChE monomer (highlighted in green throughout).

Figure 2

Model of class 1 and class 5 steric zippers. The orientation of a β-strand is shown as a block arrow. The first sheet is shown with black arrows and the second sheet with gray arrows.

Figure 3

Secondary structure of the protein chains over the course of a simulation: (A) AChE−PRAD complex, (B) AChE tetramer without PRAD, and (C) AChE monomer. The N-terminus is at the bottom and the C-terminus at the top of each secondary structure plot. The AChE peptide region is demarcated with a pair of horizontal red lines.

Figure 4

Secondary structure of the 14-residue AChE peptide as a function of time. The simulation was started from a helical conformation. Snapshots of the peptide structure at 100, 200, 300, 400, and 500 ns are also shown.

Figure 5

Conformation of class 1 and class 5 AChE zipper assemblies at the end of 100 ns simulations.