Binding of Congo red to amyloid protofibrils of the Alzheimer Aβ(9-40) peptide probed by molecular dynamics simulations

Abstract

Congo red (CR) is a commonly used histological amyloid dye and a weak amyloid inhibitor. There is currently no experimentally available structure of CR bound to an amyloid fibril and the binding modes, and the mechanisms governing its inhibitory and optical properties are poorly understood. In this work, we present the first, to our knowledge, atomistically detailed picture of CR binding to protofibrils of the Alzheimer Aβ(9-40) peptide. We identify three major binding modes, with the primary mode residing in the grooves formed by the β-sheets, and observe a restriction of the torsional rotation of the CR molecule upon binding. Our simulations reveal a novel, to our knowledge, electrostatic steering mechanism that plays an important role in the initial recognition and binding of CR to the positively charged surface residues of the fibril. Our simulations provide new, to our knowledge, insights into the striking spectrophotometric and inhibitory properties of CR. In particular, we show that birefringence upon CR binding is due to the anisotropic orientation of the CR dipoles resulting from the spatial ordering of these molecules in the grooves along the fibril axis. The fluorescent enhancement of the bound CR, in turn, is associated with the torsional restriction of this molecule upon binding.

Figure 1

Chemical structure of CR molecule. The central torsion angle (Φ) is indicated.

Figure 2

Structure of an Aβ_9–40 protofibril from the solid NMR studies. (A) A single Aβ_9–40 peptide in the protofibrils consists of a C-terminal β-strand (upper, residues 30–40), an N-terminal β-strand (lower, residues 10–22), and a loop. Residues 1–8 are disordered and thus omitted. (B) A protofibril, composed of six peptides. Negatively charged, positively charged, polar, and hydrophobic residues are colored in red, blue, green, and black, respectively.

Figure 3

Snapshots showing the initial (A and B) and the last (C) contacts between each CR molecule and the protofibril in a typical binding trajectory having two CR molecules.

Figure 4

Seven binding sites (A–G) observed from the binding simulations. Abundance is noted. Nt: N-terminal sheet layer; Ct: C-terminal sheet layer. For clarity, the unbound sheet layer is not shown.

Figure 5

Central torsion angle distributions of dye molecules at free and bound states (A) and dipole moment vector of dye molecule at the bound state (B).

Figure 6

Scheme for showing dipole orientation of CR molecules bound along the fibril axis (e.g., type I–IV of Fig. 4) on a β-sheet layer with helical rotation. (A) Twisting between two β-stands in a β-sheet layer. (B) Viewpoint along the fibril axis. (C) Viewpoint along the β-strand direction, which is perpendicular to the fibril axis. Arrow represents CR dipole vector direction.