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arXiv · 1808.07552

Binding Sites for Luminescent Amyloid Biomarkers from non-Biased Molecular Dynamics Simulations

Carolin König·Robin Skånberg·Ingrid Hotz·Anders Ynnerman·Patrick Norman·Mathieu Linares
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Abstract

A very stable binding site for the interaction between an pentameric oligothiophene and an amyloid-$β$(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 $ε$-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.

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Carolin König, Robin Skånberg, Ingrid Hotz, Anders Ynnerman, Patrick Norman, Mathieu Linares. 2018-08-22. Binding Sites for Luminescent Amyloid Biomarkers from non-Biased Molecular Dynamics Simulations. https://doi.org/10.1039/c8cc00105g

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