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

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

doi:10.1039/C8CC00105G

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

Chemical Physics 2018-08-24 v1 Biological Physics Biomolecules

Authors: 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- $\beta$ (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.

Keywords

molecular dynamics binding site amyloid-beta fibril oligothiophene luminescent biomarker conformation

Cite

@article{arxiv.1808.07552,
  title  = {Binding Sites for Luminescent Amyloid Biomarkers from non-Biased Molecular Dynamics Simulations},
  author = {Carolin König and Robin Skånberg and Ingrid Hotz and Anders Ynnerman and Patrick Norman and Mathieu Linares},
  journal= {arXiv preprint arXiv:1808.07552},
  year   = {2018}
}

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not peer-reviewed pre-print

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

Abstract

Keywords

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