  A very stable binding site for the interaction between an pentameric
oligothiophene and an amyloid-$\beta$(1-42) fibril has been identified by means
of non-biased molecular dynamics simulations. In this site, the probe is locked
in an all-trans conformation with a Coulombic binding energy of 1,200 kJ/mol
due to the interactions between the anionic carboxyl groups of the probe and
the cationic $\epsilon$-amino groups in the lysine side chain. Upon binding,
the conformationally restricted probes show a pronounced increase in molecular
planarity. This is in-line with the observed changes in luminescence properties
that serve as the foundation for their use as biomarkers.

Chemical Physics;Biological Physics;Biomolecules