Uncovering the Networks of Topological Neighborhoods in β-Strand and Amyloid β-Sheet Structures

Abstract

Although multiple hydrophobic, aromatic π-π, and electrostatic interactions are proposed to be involved in amyloid fibril formation, the precise interactions within amyloid structures remain poorly understood. Here, we carried out detailed quantum theory of atoms-in-molecules (QTAIM) analysis to examine the hydrophobic core of amyloid parallel and antiparallel β-sheet structures, and found the presence of multiple inter-strand and intra-strand topological neighborhoods, represented by networks of through-space bond paths. Similar bond paths from side chain to side chain and from side chain to main chain were found in a single β-strand and in di- and tripeptides. Some of these bond-path networks were enhanced upon β-sheet formation. Overall, our results indicate that the cumulative network of weak interactions, including various types of hydrogen bonding (X-H-Y; X, Y = H, C, O, N, S), as well as non-H-non-H bond paths, is characteristic of amyloid β-sheet structure. The present study postulated that the presence of multiple through-space bond-paths, which are local and directional, can coincide with the attractive proximity effect in forming peptide assemblies. This is consistent with a new view of the van der Waals (vdW) interactions, one of the origins of hydrophobic interaction, which is updating to be a directional intermolecular force.

Figure 1

Configurations of the side chain.

Figure 2

Leu dipeptide (Ac-Leu-NHMe) in water and in chloroform.

Figure 3

Aromatic dipeptides, Phe dipeptide in water and in chloroform.

Figure 4

Aromatic dipeptides, Trp dipeptide in water and in chloroform.

Figure 5

Bond paths in tri-peptides.

Figure 6

Molecular structures and molecular graphs. (a) Ribbon representations of amyloid parallel β-sheets and anti-parallel β-sheets. (b) Fragment of amyloid parallel β-sheets (c,d) a composition of parallel β-sheets, identical amino acid sequences of sequence 1 (c) and sequence 2 (d): Ac-Lys¹⁶-Leu¹⁷-Val¹⁸-Phe¹⁹-Phe²⁰-Ala²¹-NH₂. (e) Fragment of amyloid anti-parallel β-sheet. (f) Sequence 3: Ac-Lys¹⁶-Leu¹⁷-Val¹⁸-Phe¹⁹-Phe²⁰-Ala²¹-Asn²²-NH₂; (g) Sequence 4: NH₂-Glu²²-Ala²¹-Phe²⁰-Phe¹⁹-Val¹⁸-Leu¹⁷-Lys¹⁶- Ac.